library(knitr)
packageVersion("knitr")
## [1] '1.20'
library(energy)
packageVersion("energy")
## [1] '1.7.5'
library(broom)
packageVersion("broom")
## [1] '0.5.0'
library(plyr)
packageVersion("plyr")
## [1] '1.8.4'
library(kableExtra)
packageVersion("kableExtra")
## [1] '0.9.0'
library(foreach)
packageVersion("foreach")
## [1] '1.4.4'
library(doParallel)
## Loading required package: iterators
## Loading required package: parallel
packageVersion("doParallel")
## [1] '1.0.14'
set.seed(0)
We use the colapsed symbols to genes expression data for expressions. GSEA uses a chip functoin for connecting the uncollapsed to collapsed data. I am currently figuring out how ti perfprms that step. For now not collapsing serves the purpose. Genotypes are 33 mutants and 17 wild types. Pathways are read as done is GSEA. To remain consistent with GSEA we remove the pathways with sizes below 15 and above 500 as well as pathways that have less than 15 genes present in inside the expression matrix.
expressions <- read.csv("./GSEA leukemia/Leukemia_collapsed_symbols_for_R.csv", sep = ",", row.names = 1)
genotypes <- read.csv("./GSEA leukemia/Leukemia_genotype.txt", sep=" ", header = F)
genotypes <- as.vector(unname(ifelse( genotypes=="ALL",1,0)))
gene_names <- rownames(expressions)
expressions <- expressions[-1]
expressions <- t(expressions)
dim(expressions)
## [1] 48 10056
# pathway <- read.csv("./msigdb_v6.2_files_to_download_locally/msigdb_v6.2_GMTs_R/positional gene sets/c1.all.v6.2.symbols.csv", sep = ",", row.names = 1,na.strings = "", colClasses="character")
pathway <- read.csv("./msigdb_v6.2_files_to_download_locally/msigdb_v6.2_GMTs_R/curated gene sets/c2.all.v6.2.symbols.csv", sep = ",", row.names = 1,na.strings = "", colClasses="character")
pathway <- pathway[,-1]
pathway <- t(pathway)
row.names(pathway) <- NULL
pathway <- as.data.frame(pathway)
pathway=lapply(pathway, function(x) x[!is.na(x)] )
pathway=lapply(pathway, function(x) as.character(x))
pathway_collapsed <- pathway[sapply(pathway,function(x) {(15 <= length(x)) &&(length(x) <= 500)&& sum(colnames(expressions)%in%x)>15})]
min(sapply(pathway_collapsed,length))
## [1] 16
individual_pathway_length <- sapply(pathway_collapsed,length)
gene_number <- length(gene_names)
pathway_number <- length(individual_pathway_length)
GSEA was separately run and the enrichment results are saved. We upload the results and select the significant findings.
gsea_results <- read.csv("./GSEA leukemia/gsea_leukimia_enrichment_results6.2_curated.csv", sep = ",", row.names = 1)
# rownames(gsea_results) <- tolower(rownames(gsea_results))
gsea_results_significant <- subset(gsea_results, NOM.p.val <0.05 )
Expressions concordant with specific pathways are chosen and dcor and univariate t.test are applied on them. The univariate test is adjusted for FDR correction.
dcor_results <- list()
univariate_results <- list()
univariate_results_adjusted <- list()
for (ii in 1:length(pathway_collapsed)){
pathway_expressions <- expressions[,colnames(expressions)%in% pathway_collapsed[[ii]]]
dcor_results[ii] <- dcor((pathway_expressions),(genotypes))
}
names(dcor_results) <- names( pathway_collapsed)
set.seed(0)
# surrogate_dcor <- list()
num_simulation <- 999
cl<-makeCluster(6)
registerDoParallel(cl)
surrogate_dcor <- foreach (ii = 1:pathway_number, .export = c("num_simulation","gene_number","individual_pathway_length","genotypes"), .packages = "energy") %dopar%{
if(ii%%100==0) print(ii)
aux_dcor <- NULL
for ( jj in 1: num_simulation)
{
aux_genes <- sample(1:gene_number,individual_pathway_length[ii])
aux_dcor[jj] <- dcor(expressions[,aux_genes],genotypes)
}
# surrogate_dcor[[ii]] <- aux_dcor
aux_dcor
}
## Warning in e$fun(obj, substitute(ex), parent.frame(), e$data):
## already exporting variable(s): num_simulation, gene_number,
## individual_pathway_length, genotypes
stopCluster(cl)
nominal_dcor_pvalues <- sapply(1:pathway_number, function(x) (1+(sum(surrogate_dcor[[x]]>dcor_results[x])))/(1+num_simulation))
names(nominal_dcor_pvalues) <- names( pathway_collapsed)
head(sort(nominal_dcor_pvalues),10)
## AIGNER_ZEB1_TARGETS
## 0.001
## HADDAD_B_LYMPHOCYTE_PROGENITOR
## 0.001
## SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A12
## 0.001
## ROME_INSULIN_TARGETS_IN_MUSCLE_DN
## 0.001
## POOLA_INVASIVE_BREAST_CANCER_UP
## 0.001
## YAGI_AML_WITH_11Q23_REARRANGED
## 0.001
## DELACROIX_RAR_BOUND_ES
## 0.001
## RAO_BOUND_BY_SALL4
## 0.001
## REACTOME_CLASS_A1_RHODOPSIN_LIKE_RECEPTORS
## 0.002
## SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP
## 0.002
dcor_significant_pathways_p.value <- sort(nominal_dcor_pvalues[nominal_dcor_pvalues <0.05])
nominal_dcor_q_values <- p.adjust(nominal_dcor_pvalues , method = "fdr")
# nominal_dcor_q_values
nominal_dcor_q_values_under_25 <- sort(nominal_dcor_q_values[nominal_dcor_q_values<0.25])
nominal_dcor_q_values_under_25
## named numeric(0)
Mutually_identified_in_GSEA_dcor <- intersect(names(dcor_significant_pathways_p.value), rownames(gsea_results_significant))
Mutually_identified_in_GSEA_dcor
## [1] "HADDAD_B_LYMPHOCYTE_PROGENITOR"
## [2] "RAO_BOUND_BY_SALL4"
## [3] "BORCZUK_MALIGNANT_MESOTHELIOMA_DN"
## [4] "GOLUB_ALL_VS_AML_UP"
## [5] "HUMMEL_BURKITTS_LYMPHOMA_UP"
## [6] "KLEIN_TARGETS_OF_BCR_ABL1_FUSION"
## [7] "PASQUALUCCI_LYMPHOMA_BY_GC_STAGE_DN"
## [8] "REACTOME_ANTIGEN_ACTIVATES_B_CELL_RECEPTOR_LEADING_TO_GENERATION_OF_SECOND_MESSENGERS"
## [9] "REACTOME_GPCR_LIGAND_BINDING"
## [10] "KLEIN_PRIMARY_EFFUSION_LYMPHOMA_DN"
## [11] "VALK_AML_CLUSTER_1"
## [12] "BIOCARTA_CTCF_PATHWAY"
## [13] "KEGG_PRIMARY_IMMUNODEFICIENCY"
## [14] "SIG_PIP3_SIGNALING_IN_B_LYMPHOCYTES"
## [15] "HOLLMANN_APOPTOSIS_VIA_CD40_DN"
## [16] "WANG_CLIM2_TARGETS_DN"
## [17] "PROVENZANI_METASTASIS_UP"
## [18] "BROWN_MYELOID_CELL_DEVELOPMENT_UP"
## [19] "HOSHIDA_LIVER_CANCER_SURVIVAL_UP"
## [20] "BAELDE_DIABETIC_NEPHROPATHY_DN"
## [21] "SESTO_RESPONSE_TO_UV_C5"
## [22] "SIG_BCR_SIGNALING_PATHWAY"
## [23] "RIZKI_TUMOR_INVASIVENESS_2D_UP"
## [24] "REACTOME_SIGNALING_BY_THE_B_CELL_RECEPTOR_BCR"
## [25] "BHAT_ESR1_TARGETS_VIA_AKT1_DN"
## [26] "BASSO_CD40_SIGNALING_DN"
## [27] "PARK_HSC_AND_MULTIPOTENT_PROGENITORS"
## [28] "LEE_RECENT_THYMIC_EMIGRANT"
## [29] "LABBE_WNT3A_TARGETS_UP"
## [30] "CHESLER_BRAIN_HIGHEST_GENETIC_VARIANCE"
## [31] "HAMAI_APOPTOSIS_VIA_TRAIL_DN"
## [32] "BILANGES_SERUM_SENSITIVE_VIA_TSC2"
## [33] "NOUZOVA_TRETINOIN_AND_H4_ACETYLATION"
## [34] "LEE_LIVER_CANCER_E2F1_UP"
## [35] "BOYLAN_MULTIPLE_MYELOMA_PCA3_DN"
## [36] "ZHAN_MULTIPLE_MYELOMA_PR_DN"
## [37] "BAKKER_FOXO3_TARGETS_DN"
## [38] "CROMER_METASTASIS_UP"
## [39] "REACTOME_PI_METABOLISM"
## [40] "ST_B_CELL_ANTIGEN_RECEPTOR"
## [41] "PID_BCR_5PATHWAY"
## [42] "PID_BETA_CATENIN_NUC_PATHWAY"
## [43] "CHESLER_BRAIN_QTL_CIS"
Significant_in_dcor_not_in_GSEA <- setdiff(names(dcor_significant_pathways_p.value),Mutually_identified_in_GSEA_dcor)
pvalue_of_disparities <- rbind(dcor_significant_pathways_p.value[Significant_in_dcor_not_in_GSEA],gsea_results[Significant_in_dcor_not_in_GSEA,]$NOM.p.val)
rownames(pvalue_of_disparities) <- c("MPEA","GSEA")
pvalue_of_disparities%>%
kable("html", digits = 4, longtable = TRUE) %>%
kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
row_spec(0, angle = -0)
| AIGNER_ZEB1_TARGETS | SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A12 | ROME_INSULIN_TARGETS_IN_MUSCLE_DN | POOLA_INVASIVE_BREAST_CANCER_UP | YAGI_AML_WITH_11Q23_REARRANGED | DELACROIX_RAR_BOUND_ES | REACTOME_CLASS_A1_RHODOPSIN_LIKE_RECEPTORS | SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP | JI_METASTASIS_REPRESSED_BY_STK11 | SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN | HOELZEL_NF1_TARGETS_DN | DUTERTRE_ESTRADIOL_RESPONSE_6HR_DN | PASINI_SUZ12_TARGETS_UP | REACTOME_PEPTIDE_LIGAND_BINDING_RECEPTORS | ROY_WOUND_BLOOD_VESSEL_DN | IVANOVA_HEMATOPOIESIS_STEM_CELL_SHORT_TERM | TSENG_ADIPOGENIC_POTENTIAL_UP | SMID_BREAST_CANCER_NORMAL_LIKE_UP | AMIT_SERUM_RESPONSE_480_MCF10A | MAHADEVAN_IMATINIB_RESISTANCE_DN | INGRAM_SHH_TARGETS_DN | RORIE_TARGETS_OF_EWSR1_FLI1_FUSION_DN | DACOSTA_UV_RESPONSE_VIA_ERCC3_TTD_UP | DAWSON_METHYLATED_IN_LYMPHOMA_TCL1 | KUMAR_TARGETS_OF_MLL_AF9_FUSION | DE_YY1_TARGETS_DN | COATES_MACROPHAGE_M1_VS_M2_DN | XU_GH1_AUTOCRINE_TARGETS_UP | CHIARETTI_T_ALL_REFRACTORY_TO_THERAPY | BURTON_ADIPOGENESIS_11 | LABBE_WNT3A_TARGETS_DN | VANTVEER_BREAST_CANCER_BRCA1_UP | FERRANDO_HOX11_NEIGHBORS | SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP | PENG_RAPAMYCIN_RESPONSE_UP | BONOME_OVARIAN_CANCER_SURVIVAL_OPTIMAL_DEBULKING | GRADE_COLON_VS_RECTAL_CANCER_DN | REACTOME_G_ALPHA_I_SIGNALLING_EVENTS | REACTOME_L1CAM_INTERACTIONS | JAEGER_METASTASIS_UP | SCHLOSSER_MYC_AND_SERUM_RESPONSE_SYNERGY | ZHAN_MULTIPLE_MYELOMA_CD2_UP | KAMMINGA_SENESCENCE | MANN_RESPONSE_TO_AMIFOSTINE_UP | PETRETTO_CARDIAC_HYPERTROPHY | SANSOM_APC_TARGETS_DN | HANN_RESISTANCE_TO_BCL2_INHIBITOR_UP | TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_DN | RIGGI_EWING_SARCOMA_PROGENITOR_DN | BAUS_TFF2_TARGETS_UP | MISHRA_CARCINOMA_ASSOCIATED_FIBROBLAST_DN | HECKER_IFNB1_TARGETS | LIU_SOX4_TARGETS_UP | BOCHKIS_FOXA2_TARGETS | SIMBULAN_PARP1_TARGETS_DN | ONO_FOXP3_TARGETS_DN | HOLLERN_EMT_BREAST_TUMOR_DN | WONG_IFNA2_RESISTANCE_DN | GRESHOCK_CANCER_COPY_NUMBER_UP | MARIADASON_REGULATED_BY_HISTONE_ACETYLATION_DN | ONO_AML1_TARGETS_DN | CHANG_IMMORTALIZED_BY_HPV31_UP | FUJII_YBX1_TARGETS_DN | SMID_BREAST_CANCER_RELAPSE_IN_BONE_DN | REACTOME_CHEMOKINE_RECEPTORS_BIND_CHEMOKINES | GRAHAM_CML_QUIESCENT_VS_NORMAL_QUIESCENT_DN | DELLA_RESPONSE_TO_TSA_AND_BUTYRATE | BURTON_ADIPOGENESIS_7 | BOYAULT_LIVER_CANCER_SUBCLASS_G6_UP | HOSHIDA_LIVER_CANCER_LATE_RECURRENCE_UP | PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_4 | YANG_BREAST_CANCER_ESR1_LASER_DN | XU_CREBBP_TARGETS_DN | WOO_LIVER_CANCER_RECURRENCE_UP | BOYAULT_LIVER_CANCER_SUBCLASS_G5_DN | VERHAAK_AML_WITH_NPM1_MUTATED_DN | PLASARI_TGFB1_TARGETS_10HR_DN | DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_UP | QI_PLASMACYTOMA_UP | SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A5 | YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_9 | WIELAND_UP_BY_HBV_INFECTION | LIU_VAV3_PROSTATE_CARCINOGENESIS_UP | REACTOME_SYNTHESIS_OF_PIPS_AT_THE_PLASMA_MEMBRANE | REACTOME_REGULATION_OF_SIGNALING_BY_CBL | VECCHI_GASTRIC_CANCER_EARLY_DN | BROWNE_HCMV_INFECTION_48HR_UP | RIZKI_TUMOR_INVASIVENESS_3D_UP | ISSAEVA_MLL2_TARGETS | JOHNSTONE_PARVB_TARGETS_3_UP | YAMAZAKI_TCEB3_TARGETS_DN | ZHU_CMV_24_HR_DN | ZHENG_FOXP3_TARGETS_IN_THYMUS_UP | HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_UP | PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_UP | GAVIN_FOXP3_TARGETS_CLUSTER_P2 | REACTOME_NEPHRIN_INTERACTIONS | SIMBULAN_UV_RESPONSE_IMMORTALIZED_DN | BANDRES_RESPONSE_TO_CARMUSTIN_WITHOUT_MGMT_48HR_UP | AMIT_SERUM_RESPONSE_240_MCF10A | NUTT_GBM_VS_AO_GLIOMA_UP | MIKKELSEN_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3 | ALFANO_MYC_TARGETS | EBAUER_TARGETS_OF_PAX3_FOXO1_FUSION_UP | MARSON_FOXP3_TARGETS_STIMULATED_UP | LU_TUMOR_ANGIOGENESIS_UP | VERHAAK_GLIOBLASTOMA_PRONEURAL | CHENG_RESPONSE_TO_NICKEL_ACETATE | ZHAN_V1_LATE_DIFFERENTIATION_GENES_UP | REACTOME_MYOGENESIS | MORI_LARGE_PRE_BII_LYMPHOCYTE_DN | BECKER_TAMOXIFEN_RESISTANCE_DN | CHIANG_LIVER_CANCER_SUBCLASS_INTERFERON_DN | KEGG_PROTEASOME | NIELSEN_GIST_AND_SYNOVIAL_SARCOMA_DN | REACTOME_DEVELOPMENTAL_BIOLOGY | ONDER_CDH1_TARGETS_2_UP | VALK_AML_CLUSTER_15 | ZHAN_MULTIPLE_MYELOMA_HP_DN | BIOCARTA_PROTEASOME_PATHWAY | WNT_SIGNALING | REACTOME_CROSS_PRESENTATION_OF_SOLUBLE_EXOGENOUS_ANTIGENS_ENDOSOMES | IIZUKA_LIVER_CANCER_PROGRESSION_L0_L1_DN | STONER_ESOPHAGEAL_CARCINOGENESIS_UP | TAVAZOIE_METASTASIS | DANG_MYC_TARGETS_DN | JOHANSSON_GLIOMAGENESIS_BY_PDGFB_UP | LIAO_HAVE_SOX4_BINDING_SITES | LEE_LIVER_CANCER_DENA_UP | KONDO_PROSTATE_CANCER_HCP_WITH_H3K27ME3 | SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_DN | LEE_LIVER_CANCER_ACOX1_UP | CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_DN | EBAUER_MYOGENIC_TARGETS_OF_PAX3_FOXO1_FUSION | ULE_SPLICING_VIA_NOVA2 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| MPEA | 0.0010 | 0.0010 | 0.0010 | 0.0010 | 0.0010 | 0.0010 | 0.0020 | 0.0020 | 0.002 | 0.0030 | 0.0030 | 0.0030 | 0.0030 | 0.0040 | 0.0040 | 0.0040 | 0.0040 | 0.0040 | 0.0060 | 0.0070 | 0.0070 | 0.0070 | 0.0080 | 0.0080 | 0.0080 | 0.0080 | 0.009 | 0.010 | 0.0100 | 0.0110 | 0.0110 | 0.0110 | 0.0110 | 0.0120 | 0.0120 | 0.0130 | 0.0130 | 0.0140 | 0.0140 | 0.0140 | 0.0140 | 0.014 | 0.0140 | 0.0150 | 0.0150 | 0.0150 | 0.0150 | 0.0160 | 0.0160 | 0.016 | 0.0180 | 0.0180 | 0.0190 | 0.0190 | 0.0200 | 0.0200 | 0.0200 | 0.021 | 0.0210 | 0.0220 | 0.022 | 0.0240 | 0.0240 | 0.0250 | 0.0260 | 0.0260 | 0.0260 | 0.0260 | 0.0260 | 0.0260 | 0.0260 | 0.0270 | 0.0270 | 0.0270 | 0.0280 | 0.0290 | 0.030 | 0.0310 | 0.0310 | 0.0320 | 0.032 | 0.0330 | 0.0330 | 0.0340 | 0.0340 | 0.0340 | 0.0340 | 0.0340 | 0.0340 | 0.0350 | 0.0360 | 0.0360 | 0.0360 | 0.0360 | 0.0370 | 0.0370 | 0.038 | 0.0380 | 0.0380 | 0.0390 | 0.0390 | 0.0390 | 0.039 | 0.0400 | 0.0400 | 0.0400 | 0.0400 | 0.0410 | 0.041 | 0.0420 | 0.0420 | 0.0420 | 0.0420 | 0.0430 | 0.0430 | 0.044 | 0.0440 | 0.0440 | 0.0440 | 0.0450 | 0.0450 | 0.0450 | 0.045 | 0.0450 | 0.0450 | 0.0450 | 0.047 | 0.0470 | 0.0470 | 0.0470 | 0.0480 | 0.0480 | 0.0480 | 0.0490 | 0.0490 |
| GSEA | 0.4809 | 0.5105 | 0.3888 | 0.4875 | 0.0702 | 0.1395 | 0.0682 | 0.8162 | 0.192 | 0.5824 | 0.3519 | 0.1916 | 0.0672 | 0.0564 | 0.5845 | 0.0529 | 0.3188 | 0.1841 | 0.1279 | 0.3295 | 0.2769 | 0.7079 | 0.3265 | 0.3961 | 0.1954 | 0.2147 | 0.300 | 0.298 | 0.0691 | 0.0651 | 0.5168 | 0.1065 | 0.0564 | 0.9006 | 0.1085 | 0.7449 | 0.5645 | 0.1561 | 0.6263 | 0.3683 | 0.6918 | 0.217 | 0.1755 | 0.5238 | 0.7196 | 0.1734 | 0.2031 | 0.5068 | 0.6667 | 0.081 | 0.4853 | 0.6047 | 0.0602 | 0.3613 | 0.3727 | 0.2275 | 0.9075 | 0.284 | 0.0885 | 0.3168 | 0.072 | 0.5835 | 0.1085 | 0.3451 | 0.1042 | 0.1303 | 0.1731 | 0.3477 | 0.1896 | 0.2344 | 0.1727 | 0.1837 | 0.2589 | 0.4962 | 0.5156 | 0.1695 | 0.524 | 0.4118 | 0.1319 | 0.1708 | 0.264 | 0.1453 | 0.4482 | 0.0861 | 0.4766 | 0.4693 | 0.2675 | 0.2994 | 0.4442 | 0.1159 | 0.1111 | 0.1957 | 0.0606 | 0.4462 | 0.1184 | 0.2308 | 0.072 | 0.7152 | 0.2643 | 0.2879 | 0.1238 | 0.2605 | 0.578 | 0.5869 | 0.8472 | 0.2337 | 0.5312 | 0.4347 | 0.176 | 0.2089 | 0.5494 | 0.6851 | 0.6854 | 0.0664 | 0.0668 | 0.739 | 0.8323 | 0.4981 | 0.1946 | 0.1205 | 0.4738 | 0.0916 | 0.753 | 0.1761 | 0.9189 | 0.2945 | 0.483 | 0.2927 | 0.1016 | 0.7425 | 0.5703 | 0.2838 | 0.5545 | 0.7992 | 0.9552 |
Significant_in_GSEA_not_in_dcor <- setdiff(rownames(gsea_results_significant),Mutually_identified_in_GSEA_dcor)
pvalue_of_disparities <- rbind(nominal_dcor_pvalues[Significant_in_GSEA_not_in_dcor],gsea_results[Significant_in_GSEA_not_in_dcor,]$NOM.p.val)
rownames(pvalue_of_disparities) <- c("MPEA","GSEA")
pvalue_of_disparities %>%
kable("html", digits = 4, longtable = TRUE) %>%
kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
row_spec(0, angle = -0)
| BOGNI_TREATMENT_RELATED_MYELOID_LEUKEMIA_DN | FAELT_B_CLL_WITH_VH_REARRANGEMENTS_DN | DACOSTA_UV_RESPONSE_VIA_ERCC3_COMMON_DN | PUJANA_BRCA2_PCC_NETWORK | KEGG_BASE_EXCISION_REPAIR | REACTOME_ANTIVIRAL_MECHANISM_BY_IFN_STIMULATED_GENES | REACTOME_CELL_CYCLE | GARY_CD5_TARGETS_DN | MARIADASON_RESPONSE_TO_BUTYRATE_SULINDAC_6 | DAZARD_RESPONSE_TO_UV_NHEK_DN | BENPORATH_PROLIFERATION | NA | KEGG_B_CELL_RECEPTOR_SIGNALING_PATHWAY | REACTOME_REGULATION_OF_GLUCOKINASE_BY_GLUCOKINASE_REGULATORY_PROTEIN | RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_UP | RAMALHO_STEMNESS_UP | DING_LUNG_CANCER_EXPRESSION_BY_COPY_NUMBER | REACTOME_CELL_CYCLE_CHECKPOINTS | REACTOME_ANTIGEN_PROCESSING_UBIQUITINATION_PROTEASOME_DEGRADATION | GENTILE_UV_RESPONSE_CLUSTER_D8 | MORI_EMU_MYC_LYMPHOMA_BY_ONSET_TIME_UP | REACTOME_HIV_LIFE_CYCLE | NA | REACTOME_HIV_INFECTION | REACTOME_CHROMOSOME_MAINTENANCE | FIGUEROA_AML_METHYLATION_CLUSTER_1_DN | ZHANG_BREAST_CANCER_PROGENITORS_UP | PYEON_HPV_POSITIVE_TUMORS_UP | MOREAUX_MULTIPLE_MYELOMA_BY_TACI_DN | CHIANG_LIVER_CANCER_SUBCLASS_PROLIFERATION_UP | NA | SHEN_SMARCA2_TARGETS_UP | GRADE_METASTASIS_DN | NA | REACTOME_BASE_EXCISION_REPAIR | REACTOME_CELL_CYCLE_MITOTIC | REACTOME_TRANSCRIPTION | KAUFFMANN_DNA_REPAIR_GENES | ZHAN_MULTIPLE_MYELOMA_CD1_VS_CD2_DN | KEGG_ANTIGEN_PROCESSING_AND_PRESENTATION | STARK_PREFRONTAL_CORTEX_22Q11_DELETION_UP | MITSIADES_RESPONSE_TO_APLIDIN_DN | REACTOME_HOST_INTERACTIONS_OF_HIV_FACTORS | BOYLAN_MULTIPLE_MYELOMA_C_D_UP | NA | REACTOME_NEP_NS2_INTERACTS_WITH_THE_CELLULAR_EXPORT_MACHINERY | REACTOME_TELOMERE_MAINTENANCE | BIDUS_METASTASIS_UP | ZHANG_TLX_TARGETS_36HR_DN | MARTINEZ_RESPONSE_TO_TRABECTEDIN_DN | SHAFFER_IRF4_TARGETS_IN_ACTIVATED_DENDRITIC_CELL | KIM_WT1_TARGETS_DN | MORI_PLASMA_CELL_DN | ENK_UV_RESPONSE_KERATINOCYTE_DN | ZHAN_EARLY_DIFFERENTIATION_GENES_DN | REACTOME_APC_C_CDC20_MEDIATED_DEGRADATION_OF_MITOTIC_PROTEINS | OISHI_CHOLANGIOMA_STEM_CELL_LIKE_UP | MATTIOLI_MGUS_VS_PCL | ABRAMSON_INTERACT_WITH_AIRE | ZHAN_MULTIPLE_MYELOMA_CD1_AND_CD2_UP | VILLANUEVA_LIVER_CANCER_KRT19_UP | REACTOME_LATE_PHASE_OF_HIV_LIFE_CYCLE | KEGG_SPLICEOSOME | MORI_MATURE_B_LYMPHOCYTE_DN | DITTMER_PTHLH_TARGETS_DN | CAIRO_HEPATOBLASTOMA_UP | BIOCARTA_BCR_PATHWAY | REACTOME_MRNA_PROCESSING | NA | ROSS_AML_WITH_AML1_ETO_FUSION | REACTOME_GLUCOSE_TRANSPORT | REACTOME_APC_C_CDH1_MEDIATED_DEGRADATION_OF_CDC20_AND_OTHER_APC_C_CDH1_TARGETED_PROTEINS_IN_LATE_MITOSIS_EARLY_G1 | REACTOME_DEPOSITION_OF_NEW_CENPA_CONTAINING_NUCLEOSOMES_AT_THE_CENTROMERE | PECE_MAMMARY_STEM_CELL_DN | DAZARD_UV_RESPONSE_CLUSTER_G6 | GENTILE_UV_RESPONSE_CLUSTER_D4 | REACTOME_METABOLISM_OF_NON_CODING_RNA | REACTOME_REGULATION_OF_MITOTIC_CELL_CYCLE | KAMMINGA_EZH2_TARGETS | NA | HEDENFALK_BREAST_CANCER_BRCA1_VS_BRCA2 | BROWNE_HCMV_INFECTION_10HR_DN | PEART_HDAC_PROLIFERATION_CLUSTER_UP | PELLICCIOTTA_HDAC_IN_ANTIGEN_PRESENTATION_DN | REACTOME_P53_DEPENDENT_G1_DNA_DAMAGE_RESPONSE | GALE_APL_WITH_FLT3_MUTATED_UP | REACTOME_AUTODEGRADATION_OF_CDH1_BY_CDH1_APC_C | HAHTOLA_MYCOSIS_FUNGOIDES_CD4_DN | HEDENFALK_BREAST_CANCER_HEREDITARY_VS_SPORADIC | BIOCARTA_CARM_ER_PATHWAY | REACTOME_CLASS_I_MHC_MEDIATED_ANTIGEN_PROCESSING_PRESENTATION | VALK_AML_CLUSTER_10 | NA | NA | BIOCARTA_PAR1_PATHWAY | SESTO_RESPONSE_TO_UV_C2 | CARD_MIR302A_TARGETS | REACTOME_SCF_BETA_TRCP_MEDIATED_DEGRADATION_OF_EMI1 | REACTOME_AUTODEGRADATION_OF_THE_E3_UBIQUITIN_LIGASE_COP1 | REACTOME_RNA_POL_I_RNA_POL_III_AND_MITOCHONDRIAL_TRANSCRIPTION | ELLWOOD_MYC_TARGETS_DN | NA | KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_GAMMA_IN_WS | BROWNE_HCMV_INFECTION_4HR_DN | PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_UP | WAKASUGI_HAVE_ZNF143_BINDING_SITES | NA | ROESSLER_LIVER_CANCER_METASTASIS_DN | REACTOME_TRANSPORT_OF_MATURE_MRNA_DERIVED_FROM_AN_INTRONLESS_TRANSCRIPT | REACTOME_P53_INDEPENDENT_G1_S_DNA_DAMAGE_CHECKPOINT | REACTOME_NOTCH1_INTRACELLULAR_DOMAIN_REGULATES_TRANSCRIPTION | BENPORATH_ES_1 | PID_EPHA2_FWD_PATHWAY | REACTOME_RNA_POL_I_TRANSCRIPTION | YANG_BREAST_CANCER_ESR1_DN | REACTOME_MEIOSIS | REACTOME_REGULATION_OF_ORNITHINE_DECARBOXYLASE_ODC | BOYLAN_MULTIPLE_MYELOMA_C_UP | KEGG_SNARE_INTERACTIONS_IN_VESICULAR_TRANSPORT | HOLLMANN_APOPTOSIS_VIA_CD40_UP | WHITFIELD_CELL_CYCLE_G2_M | BRUINS_UVC_RESPONSE_MIDDLE | PID_P38_MK2_PATHWAY | KYNG_WERNER_SYNDROM_AND_NORMAL_AGING_UP | CHENG_IMPRINTED_BY_ESTRADIOL | NA | RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_MODERATELY_UP | TIEN_INTESTINE_PROBIOTICS_2HR_DN | ZUCCHI_METASTASIS_UP | PID_P53_REGULATION_PATHWAY | BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_CIS | REACTOME_TRANSPORT_OF_RIBONUCLEOPROTEINS_INTO_THE_HOST_NUCLEUS | KIM_GERMINAL_CENTER_T_HELPER_UP | PID_PS1_PATHWAY | OUILLETTE_CLL_13Q14_DELETION_UP | THUM_SYSTOLIC_HEART_FAILURE_DN | REACTOME_APOPTOSIS | PID_AR_NONGENOMIC_PATHWAY | ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_UP | JI_RESPONSE_TO_FSH_UP | BOYAULT_LIVER_CANCER_SUBCLASS_G1_UP | SIG_CHEMOTAXIS | BRUINS_UVC_RESPONSE_EARLY_LATE | LIN_MELANOMA_COPY_NUMBER_DN | NA | JOHNSTONE_PARVB_TARGETS_2_DN | NA | KYNG_ENVIRONMENTAL_STRESS_RESPONSE_UP | LAIHO_COLORECTAL_CANCER_SERRATED_DN | PID_HEDGEHOG_GLI_PATHWAY | LINDGREN_BLADDER_CANCER_WITH_LOH_IN_CHR9Q | LIN_MELANOMA_COPY_NUMBER_UP | DAVICIONI_MOLECULAR_ARMS_VS_ERMS_UP | HAHTOLA_MYCOSIS_FUNGOIDES_SKIN_UP | BIOCARTA_TFF_PATHWAY | HOSHIDA_LIVER_CANCER_SUBCLASS_S2 | BENPORATH_OCT4_TARGETS | GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_UP | NA | SETLUR_PROSTATE_CANCER_TMPRSS2_ERG_FUSION_UP | NA | KUROKAWA_LIVER_CANCER_CHEMOTHERAPY_DN | BILD_E2F3_ONCOGENIC_SIGNATURE | NA | WOOD_EBV_EBNA1_TARGETS_DN | NA | WINTER_HYPOXIA_DN | IKEDA_MIR30_TARGETS_UP | REACTOME_NRAGE_SIGNALS_DEATH_THROUGH_JNK | KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_UV_IN_OLD | HASLINGER_B_CLL_WITH_6Q21_DELETION | BIOCARTA_WNT_PATHWAY | YAGI_AML_WITH_T_9_11_TRANSLOCATION | HIRSCH_CELLULAR_TRANSFORMATION_SIGNATURE_DN | BIOCARTA_CXCR4_PATHWAY | TAYLOR_METHYLATED_IN_ACUTE_LYMPHOBLASTIC_LEUKEMIA | GINESTIER_BREAST_CANCER_20Q13_AMPLIFICATION_UP | ZHANG_RESPONSE_TO_IKK_INHIBITOR_AND_TNF_DN | ZHAN_MULTIPLE_MYELOMA_HP_UP | REACTOME_SMAD2_SMAD3_SMAD4_HETEROTRIMER_REGULATES_TRANSCRIPTION | MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_DN | VANHARANTA_UTERINE_FIBROID_WITH_7Q_DELETION_UP | NA | BILBAN_B_CLL_LPL_UP | CHEN_NEUROBLASTOMA_COPY_NUMBER_GAINS | KEGG_NOTCH_SIGNALING_PATHWAY | HADDAD_T_LYMPHOCYTE_AND_NK_PROGENITOR_UP | LEE_CALORIE_RESTRICTION_MUSCLE_DN | KYNG_DNA_DAMAGE_BY_GAMMA_AND_UV_RADIATION | KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS | KATSANOU_ELAVL1_TARGETS_DN | GYORFFY_MITOXANTRONE_RESISTANCE | MULLIGHAN_NPM1_SIGNATURE_3_DN | JIANG_TIP30_TARGETS_UP | REACTOME_APOPTOTIC_CLEAVAGE_OF_CELLULAR_PROTEINS | GRYDER_PAX3FOXO1_ENHANCERS_KO_DOWN | CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_2 | HOFMANN_CELL_LYMPHOMA_UP | STAMBOLSKY_RESPONSE_TO_VITAMIN_D3_UP | ABBUD_LIF_SIGNALING_1_UP | DEBOSSCHER_NFKB_TARGETS_REPRESSED_BY_GLUCOCORTICOIDS | CHEOK_RESPONSE_TO_HD_MTX_UP | REACTOME_PHASE1_FUNCTIONALIZATION_OF_COMPOUNDS | VERHAAK_AML_WITH_NPM1_MUTATED_UP | PID_INTEGRIN_CS_PATHWAY | PID_UPA_UPAR_PATHWAY | REACTOME_COLLAGEN_FORMATION | DALESSIO_TSA_RESPONSE | GUENTHER_GROWTH_SPHERICAL_VS_ADHERENT_DN | VERRECCHIA_EARLY_RESPONSE_TO_TGFB1 | BIOCARTA_DC_PATHWAY | NAKAJIMA_MAST_CELL | REACTOME_CYTOCHROME_P450_ARRANGED_BY_SUBSTRATE_TYPE | KIM_ALL_DISORDERS_CALB1_CORR_DN | GOLUB_ALL_VS_AML_DN | PID_INTEGRIN2_PATHWAY | HESS_TARGETS_OF_HOXA9_AND_MEIS1_DN | LIAN_NEUTROPHIL_GRANULE_CONSTITUENTS | KRIEG_HYPOXIA_VIA_KDM3A | PID_SYNDECAN_1_PATHWAY | PARK_APL_PATHOGENESIS_DN | HWANG_PROSTATE_CANCER_MARKERS | NA | AMIT_EGF_RESPONSE_120_MCF10A | LI_CISPLATIN_RESISTANCE_DN | REACTOME_CELL_SURFACE_INTERACTIONS_AT_THE_VASCULAR_WALL | VERRECCHIA_RESPONSE_TO_TGFB1_C2 | GROSS_ELK3_TARGETS_DN | ALTEMEIER_RESPONSE_TO_LPS_WITH_MECHANICAL_VENTILATION | NABA_COLLAGENS | GHANDHI_BYSTANDER_IRRADIATION_UP | KOHOUTEK_CCNT1_TARGETS | TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_HSC_DN | KOBAYASHI_EGFR_SIGNALING_6HR_DN | REACTOME_TRANSPORT_OF_GLUCOSE_AND_OTHER_SUGARS_BILE_SALTS_AND_ORGANIC_ACIDS_METAL_IONS_AND_AMINE_COMPOUNDS | SARTIPY_NORMAL_AT_INSULIN_RESISTANCE_UP | REACTOME_EXTRACELLULAR_MATRIX_ORGANIZATION | MIKKELSEN_MCV6_ICP_WITH_H3K27ME3 | VART_KSHV_INFECTION_ANGIOGENIC_MARKERS_UP | KEGG_ARACHIDONIC_ACID_METABOLISM | NA | ZHAN_MULTIPLE_MYELOMA_CD1_VS_CD2_UP | CHEN_LVAD_SUPPORT_OF_FAILING_HEART_UP | HOLLERN_MICROACINAR_BREAST_TUMOR_UP | WANG_BARRETTS_ESOPHAGUS_AND_ESOPHAGUS_CANCER_DN | MIKKELSEN_MEF_ICP_WITH_H3K27ME3 | GHANDHI_DIRECT_IRRADIATION_UP | BIOCARTA_CYTOKINE_PATHWAY | MIKKELSEN_MEF_LCP_WITH_H3K27ME3 | YAO_HOXA10_TARGETS_VIA_PROGESTERONE_UP | VERRECCHIA_RESPONSE_TO_TGFB1_C1 | PID_RXR_VDR_PATHWAY | XU_HGF_SIGNALING_NOT_VIA_AKT1_6HR | WANG_CLASSIC_ADIPOGENIC_TARGETS_OF_PPARG | KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_LACTO_AND_NEOLACTO_SERIES | HUPER_BREAST_BASAL_VS_LUMINAL_UP | NAKAYAMA_SOFT_TISSUE_TUMORS_PCA2_DN | JEON_SMAD6_TARGETS_UP | PEPPER_CHRONIC_LYMPHOCYTIC_LEUKEMIA_UP | PID_INTEGRIN5_PATHWAY | NA | NAKAMURA_ADIPOGENESIS_EARLY_UP | BIOCARTA_INFLAM_PATHWAY | BERENJENO_ROCK_SIGNALING_NOT_VIA_RHOA_UP | REACTOME_INTEGRIN_CELL_SURFACE_INTERACTIONS | KHETCHOUMIAN_TRIM24_TARGETS_UP | NAKAJIMA_EOSINOPHIL | SEMENZA_HIF1_TARGETS | MOREAUX_B_LYMPHOCYTE_MATURATION_BY_TACI_UP | AMIT_EGF_RESPONSE_120_HELA | NA | FIGUEROA_AML_METHYLATION_CLUSTER_5_DN | REACTOME_AMINE_LIGAND_BINDING_RECEPTORS | SABATES_COLORECTAL_ADENOMA_UP | PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_DN | SUZUKI_RESPONSE_TO_TSA_AND_DECITABINE_1A | MADAN_DPPA4_TARGETS | URS_ADIPOCYTE_DIFFERENTIATION_UP | ONDER_CDH1_SIGNALING_VIA_CTNNB1 | KERLEY_RESPONSE_TO_CISPLATIN_UP | CREIGHTON_AKT1_SIGNALING_VIA_MTOR_UP | MEISSNER_NPC_HCP_WITH_H3K4ME2_AND_H3K27ME3 | LABBE_TARGETS_OF_TGFB1_AND_WNT3A_DN | SAKAI_CHRONIC_HEPATITIS_VS_LIVER_CANCER_DN | MARKEY_RB1_CHRONIC_LOF_DN | SHEN_SMARCA2_TARGETS_DN | NABA_ECM_AFFILIATED | KIM_LIVER_CANCER_POOR_SURVIVAL_DN | REACTOME_CLASS_B_2_SECRETIN_FAMILY_RECEPTORS | NA | WATANABE_COLON_CANCER_MSI_VS_MSS_UP | MOREAUX_MULTIPLE_MYELOMA_BY_TACI_UP | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| MPEA | 0.050 | 0.3470 | 0.2320 | 0.1090 | 0.12 | 0.5520 | 0.2540 | 0.585 | 0.0840 | 0.4770 | 0.3420 | NA | 0.072 | 0.5320 | 0.509 | 0.5880 | 0.4030 | 0.1660 | 0.2510 | 0.1000 | 0.2270 | 0.2250 | NA | 0.1860 | 0.2620 | 0.6410 | 0.4470 | 0.2140 | 0.6180 | 0.181 | NA | 0.794 | 0.058 | NA | 0.2290 | 0.3840 | 0.8390 | 0.1510 | 0.0710 | 0.1630 | 0.4250 | 0.5630 | 0.3500 | 0.6360 | NA | 0.3850 | 0.1990 | 0.8580 | 0.6180 | 0.3370 | 0.3430 | 0.3780 | 0.467 | 0.2970 | 0.1340 | 0.1130 | 0.971 | 0.1750 | 0.1480 | 0.441 | 0.8450 | 0.7590 | 0.6480 | 0.2680 | 0.5440 | 0.0920 | 0.0640 | 0.7820 | NA | 0.2480 | 0.6380 | 0.120 | 0.6350 | 0.0610 | 0.3220 | 0.3010 | 0.8120 | 0.1200 | 0.0780 | NA | 0.2330 | 0.3950 | 0.2070 | 0.0930 | 0.1060 | 0.1470 | 0.1040 | 0.2610 | 0.0750 | 0.2300 | 0.3190 | 0.0760 | NA | NA | 0.2440 | 0.2650 | 0.373 | 0.0910 | 0.0880 | 0.7830 | 0.8090 | NA | 0.2750 | 0.8380 | 0.8540 | 0.4500 | NA | 0.7940 | 0.4810 | 0.0840 | 0.872 | 0.2940 | 0.9570 | 0.708 | 0.9430 | 0.4530 | 0.0700 | 0.1980 | 0.8380 | 0.6620 | 0.8080 | 0.452 | 0.2120 | 0.4160 | 0.8100 | NA | 0.2270 | 0.3340 | 0.4440 | 0.7380 | 0.376 | 0.5720 | 0.7980 | 0.5780 | 0.4590 | 0.7000 | 0.0880 | 0.9020 | 0.795 | 0.166 | 0.6660 | 0.0960 | 0.6870 | 0.6730 | NA | 0.1430 | NA | 0.0880 | 0.512 | 0.3450 | 0.9110 | 0.2530 | 0.3530 | 0.2300 | 0.8370 | 0.4480 | 0.7330 | 0.1680 | NA | 0.4860 | NA | 0.3520 | 0.7680 | NA | 0.0890 | NA | 0.0590 | 0.1770 | 0.1010 | 0.2920 | 0.8030 | 0.0840 | 0.2730 | 0.5320 | 0.0820 | 0.6680 | 0.9720 | 0.1630 | 0.4890 | 0.7610 | 0.1140 | 0.238 | NA | 0.6730 | 0.7410 | 0.6740 | 0.2790 | 0.1420 | 0.0640 | 0.8500 | 0.0770 | 0.8600 | 0.2650 | 0.107 | 0.1680 | 0.3350 | 0.9250 | 0.3140 | 0.4780 | 0.448 | 0.4090 | 0.3340 | 0.675 | 0.4970 | 0.1520 | 0.313 | 0.84 | 0.1390 | 0.0660 | 0.2220 | 0.2290 | 0.0600 | 0.7070 | 0.6710 | 0.089 | 0.0520 | 0.5200 | 0.3800 | 0.9620 | 0.1540 | 0.2700 | 0.0690 | NA | 0.8130 | 0.745 | 0.3620 | 0.3070 | 0.744 | 0.8270 | 0.7770 | 0.678 | 0.4880 | 0.3210 | 0.832 | 0.7100 | 0.9990 | 0.6330 | 0.9920 | 0.0960 | 0.6250 | NA | 0.743 | 0.3820 | 0.1600 | 0.0970 | 0.9990 | 0.8290 | 0.4450 | 0.9480 | 0.4190 | 0.1340 | 0.5560 | 0.1910 | 0.4930 | 0.6820 | 0.9820 | 0.8510 | 0.3280 | 0.9270 | 0.2810 | NA | 0.8070 | 0.4290 | 0.9760 | 0.2380 | 0.289 | 0.2530 | 0.6670 | 0.6470 | 0.4180 | NA | 0.4470 | 0.9350 | 0.9720 | 0.1850 | 0.5870 | 0.9050 | 0.5410 | 0.6000 | 0.0690 | 0.1500 | 1.0000 | 0.9670 | 0.3630 | 0.3990 | 0.9720 | 0.4500 | 0.1790 | 0.9020 | NA | 0.947 | 0.6590 |
| GSEA | 0.006 | 0.0039 | 0.0081 | 0.0218 | 0.00 | 0.0079 | 0.0216 | 0.006 | 0.0157 | 0.0141 | 0.0426 | 0.022 | 0.002 | 0.0039 | 0.004 | 0.0139 | 0.0039 | 0.0194 | 0.0175 | 0.0041 | 0.0462 | 0.0182 | 0.0198 | 0.0158 | 0.0189 | 0.0077 | 0.0142 | 0.0197 | 0.0155 | 0.048 | 0.0347 | 0.020 | 0.018 | 0.0038 | 0.0039 | 0.0374 | 0.0059 | 0.0277 | 0.0041 | 0.0077 | 0.0062 | 0.0436 | 0.0199 | 0.0122 | 0.0335 | 0.0201 | 0.0189 | 0.0266 | 0.0283 | 0.0261 | 0.0161 | 0.0101 | 0.025 | 0.0451 | 0.0137 | 0.0294 | 0.002 | 0.0317 | 0.0385 | 0.006 | 0.0356 | 0.0242 | 0.0356 | 0.0472 | 0.0121 | 0.0061 | 0.0079 | 0.0455 | 0.0062 | 0.0059 | 0.0139 | 0.035 | 0.0245 | 0.0019 | 0.0402 | 0.0179 | 0.0258 | 0.0379 | 0.0472 | 0.0372 | 0.0277 | 0.0082 | 0.0292 | 0.0254 | 0.0409 | 0.0294 | 0.0371 | 0.0461 | 0.0329 | 0.0454 | 0.0296 | 0.0098 | 0.0126 | 0.0241 | 0.0102 | 0.0041 | 0.006 | 0.0352 | 0.0388 | 0.0214 | 0.0057 | 0.0081 | 0.0099 | 0.0061 | 0.0202 | 0.0258 | 0.0344 | 0.0198 | 0.0459 | 0.0464 | 0.032 | 0.0386 | 0.0085 | 0.041 | 0.0081 | 0.0298 | 0.0484 | 0.0205 | 0.0176 | 0.0266 | 0.0484 | 0.014 | 0.0292 | 0.0188 | 0.0102 | 0.0431 | 0.0359 | 0.0475 | 0.0371 | 0.0385 | 0.012 | 0.0466 | 0.0216 | 0.0141 | 0.0041 | 0.0141 | 0.0281 | 0.0271 | 0.000 | 0.014 | 0.0222 | 0.0021 | 0.0211 | 0.0348 | 0.0394 | 0.0346 | 0.0329 | 0.0198 | 0.045 | 0.0183 | 0.0423 | 0.0304 | 0.0202 | 0.0282 | 0.0377 | 0.0482 | 0.0103 | 0.0356 | 0.0426 | 0.0224 | 0.0266 | 0.0165 | 0.0285 | 0.0381 | 0.0217 | 0.0372 | 0.0316 | 0.0401 | 0.0311 | 0.0331 | 0.0375 | 0.0461 | 0.0319 | 0.0199 | 0.0402 | 0.0218 | 0.0275 | 0.0274 | 0.0338 | 0.0454 | 0.0276 | 0.039 | 0.0427 | 0.0476 | 0.0188 | 0.0411 | 0.0344 | 0.0381 | 0.0402 | 0.0481 | 0.0225 | 0.0406 | 0.0364 | 0.048 | 0.0447 | 0.0379 | 0.0355 | 0.0478 | 0.0473 | 0.000 | 0.0037 | 0.0019 | 0.000 | 0.0078 | 0.0059 | 0.000 | 0.00 | 0.0113 | 0.0096 | 0.0038 | 0.0038 | 0.0038 | 0.0019 | 0.0038 | 0.000 | 0.0079 | 0.0152 | 0.0056 | 0.0201 | 0.0019 | 0.0353 | 0.0113 | 0.0242 | 0.0119 | 0.018 | 0.0057 | 0.0133 | 0.019 | 0.0321 | 0.0077 | 0.028 | 0.0249 | 0.0059 | 0.015 | 0.0078 | 0.0254 | 0.0156 | 0.0169 | 0.0114 | 0.0186 | 0.0252 | 0.019 | 0.0152 | 0.0333 | 0.0296 | 0.0019 | 0.0411 | 0.0209 | 0.0152 | 0.0111 | 0.0189 | 0.0248 | 0.0273 | 0.0252 | 0.0189 | 0.0099 | 0.0135 | 0.0328 | 0.0496 | 0.0361 | 0.0418 | 0.0421 | 0.0397 | 0.0365 | 0.0376 | 0.035 | 0.0291 | 0.0474 | 0.0342 | 0.0336 | 0.0382 | 0.0301 | 0.0411 | 0.0416 | 0.0342 | 0.0483 | 0.0262 | 0.0337 | 0.0361 | 0.0216 | 0.0412 | 0.0157 | 0.0437 | 0.0366 | 0.0473 | 0.0391 | 0.0366 | 0.0476 | 0.0218 | 0.0371 | 0.049 | 0.0301 |
enrichment_ratio_dcor <- NULL
enrichment_ratio_ttest <- NULL
for ( ii in 1:length(Significant_in_dcor_not_in_GSEA) ){
aux_genes <- intersect(pathway_collapsed[[Significant_in_dcor_not_in_GSEA[[ii]]]],colnames(expressions))
aux_pathway_dcor <- dcor.test(dist(expressions[,aux_genes]),dist(genotypes),R=10000)
aux_individual_genes_in_pathway_dcor <- sapply(aux_genes,function(x) dcor.test(dist(expressions[,x]),dist(genotypes),R=10000)$p.value<0.05 )
aux_enrichment_ratio_dcor <- sum(aux_individual_genes_in_pathway_dcor)/length(aux_individual_genes_in_pathway_dcor)
enrichment_ratio_dcor[ii] <- aux_enrichment_ratio_dcor
aux_individual_genes_in_pathway_ttest <- sapply(aux_genes,function(x) t.test(expressions[,x]~genotypes)$p.value<0.05 )
aux_enrichment_ratio_ttest <- sum(aux_individual_genes_in_pathway_ttest)/length(aux_individual_genes_in_pathway_ttest)
aux_enrichment_ratio_ttest
enrichment_ratio_ttest[ii] <-aux_enrichment_ratio_ttest
}
enrichment_ratio_comparison <- rbind(enrichment_ratio_dcor,enrichment_ratio_ttest)
rownames(enrichment_ratio_comparison) <- c("MPEA","GSEA")
colnames(enrichment_ratio_comparison) <- Significant_in_dcor_not_in_GSEA
enrichment_ratio_comparison%>%
kable("html", digits = 4, longtable = TRUE) %>%
kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
row_spec(0, angle = -0)
| AIGNER_ZEB1_TARGETS | SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A12 | ROME_INSULIN_TARGETS_IN_MUSCLE_DN | POOLA_INVASIVE_BREAST_CANCER_UP | YAGI_AML_WITH_11Q23_REARRANGED | DELACROIX_RAR_BOUND_ES | REACTOME_CLASS_A1_RHODOPSIN_LIKE_RECEPTORS | SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP | JI_METASTASIS_REPRESSED_BY_STK11 | SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN | HOELZEL_NF1_TARGETS_DN | DUTERTRE_ESTRADIOL_RESPONSE_6HR_DN | PASINI_SUZ12_TARGETS_UP | REACTOME_PEPTIDE_LIGAND_BINDING_RECEPTORS | ROY_WOUND_BLOOD_VESSEL_DN | IVANOVA_HEMATOPOIESIS_STEM_CELL_SHORT_TERM | TSENG_ADIPOGENIC_POTENTIAL_UP | SMID_BREAST_CANCER_NORMAL_LIKE_UP | AMIT_SERUM_RESPONSE_480_MCF10A | MAHADEVAN_IMATINIB_RESISTANCE_DN | INGRAM_SHH_TARGETS_DN | RORIE_TARGETS_OF_EWSR1_FLI1_FUSION_DN | DACOSTA_UV_RESPONSE_VIA_ERCC3_TTD_UP | DAWSON_METHYLATED_IN_LYMPHOMA_TCL1 | KUMAR_TARGETS_OF_MLL_AF9_FUSION | DE_YY1_TARGETS_DN | COATES_MACROPHAGE_M1_VS_M2_DN | XU_GH1_AUTOCRINE_TARGETS_UP | CHIARETTI_T_ALL_REFRACTORY_TO_THERAPY | BURTON_ADIPOGENESIS_11 | LABBE_WNT3A_TARGETS_DN | VANTVEER_BREAST_CANCER_BRCA1_UP | FERRANDO_HOX11_NEIGHBORS | SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP | PENG_RAPAMYCIN_RESPONSE_UP | BONOME_OVARIAN_CANCER_SURVIVAL_OPTIMAL_DEBULKING | GRADE_COLON_VS_RECTAL_CANCER_DN | REACTOME_G_ALPHA_I_SIGNALLING_EVENTS | REACTOME_L1CAM_INTERACTIONS | JAEGER_METASTASIS_UP | SCHLOSSER_MYC_AND_SERUM_RESPONSE_SYNERGY | ZHAN_MULTIPLE_MYELOMA_CD2_UP | KAMMINGA_SENESCENCE | MANN_RESPONSE_TO_AMIFOSTINE_UP | PETRETTO_CARDIAC_HYPERTROPHY | SANSOM_APC_TARGETS_DN | HANN_RESISTANCE_TO_BCL2_INHIBITOR_UP | TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_DN | RIGGI_EWING_SARCOMA_PROGENITOR_DN | BAUS_TFF2_TARGETS_UP | MISHRA_CARCINOMA_ASSOCIATED_FIBROBLAST_DN | HECKER_IFNB1_TARGETS | LIU_SOX4_TARGETS_UP | BOCHKIS_FOXA2_TARGETS | SIMBULAN_PARP1_TARGETS_DN | ONO_FOXP3_TARGETS_DN | HOLLERN_EMT_BREAST_TUMOR_DN | WONG_IFNA2_RESISTANCE_DN | GRESHOCK_CANCER_COPY_NUMBER_UP | MARIADASON_REGULATED_BY_HISTONE_ACETYLATION_DN | ONO_AML1_TARGETS_DN | CHANG_IMMORTALIZED_BY_HPV31_UP | FUJII_YBX1_TARGETS_DN | SMID_BREAST_CANCER_RELAPSE_IN_BONE_DN | REACTOME_CHEMOKINE_RECEPTORS_BIND_CHEMOKINES | GRAHAM_CML_QUIESCENT_VS_NORMAL_QUIESCENT_DN | DELLA_RESPONSE_TO_TSA_AND_BUTYRATE | BURTON_ADIPOGENESIS_7 | BOYAULT_LIVER_CANCER_SUBCLASS_G6_UP | HOSHIDA_LIVER_CANCER_LATE_RECURRENCE_UP | PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_4 | YANG_BREAST_CANCER_ESR1_LASER_DN | XU_CREBBP_TARGETS_DN | WOO_LIVER_CANCER_RECURRENCE_UP | BOYAULT_LIVER_CANCER_SUBCLASS_G5_DN | VERHAAK_AML_WITH_NPM1_MUTATED_DN | PLASARI_TGFB1_TARGETS_10HR_DN | DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_UP | QI_PLASMACYTOMA_UP | SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A5 | YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_9 | WIELAND_UP_BY_HBV_INFECTION | LIU_VAV3_PROSTATE_CARCINOGENESIS_UP | REACTOME_SYNTHESIS_OF_PIPS_AT_THE_PLASMA_MEMBRANE | REACTOME_REGULATION_OF_SIGNALING_BY_CBL | VECCHI_GASTRIC_CANCER_EARLY_DN | BROWNE_HCMV_INFECTION_48HR_UP | RIZKI_TUMOR_INVASIVENESS_3D_UP | ISSAEVA_MLL2_TARGETS | JOHNSTONE_PARVB_TARGETS_3_UP | YAMAZAKI_TCEB3_TARGETS_DN | ZHU_CMV_24_HR_DN | ZHENG_FOXP3_TARGETS_IN_THYMUS_UP | HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_UP | PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_UP | GAVIN_FOXP3_TARGETS_CLUSTER_P2 | REACTOME_NEPHRIN_INTERACTIONS | SIMBULAN_UV_RESPONSE_IMMORTALIZED_DN | BANDRES_RESPONSE_TO_CARMUSTIN_WITHOUT_MGMT_48HR_UP | AMIT_SERUM_RESPONSE_240_MCF10A | NUTT_GBM_VS_AO_GLIOMA_UP | MIKKELSEN_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3 | ALFANO_MYC_TARGETS | EBAUER_TARGETS_OF_PAX3_FOXO1_FUSION_UP | MARSON_FOXP3_TARGETS_STIMULATED_UP | LU_TUMOR_ANGIOGENESIS_UP | VERHAAK_GLIOBLASTOMA_PRONEURAL | CHENG_RESPONSE_TO_NICKEL_ACETATE | ZHAN_V1_LATE_DIFFERENTIATION_GENES_UP | REACTOME_MYOGENESIS | MORI_LARGE_PRE_BII_LYMPHOCYTE_DN | BECKER_TAMOXIFEN_RESISTANCE_DN | CHIANG_LIVER_CANCER_SUBCLASS_INTERFERON_DN | KEGG_PROTEASOME | NIELSEN_GIST_AND_SYNOVIAL_SARCOMA_DN | REACTOME_DEVELOPMENTAL_BIOLOGY | ONDER_CDH1_TARGETS_2_UP | VALK_AML_CLUSTER_15 | ZHAN_MULTIPLE_MYELOMA_HP_DN | BIOCARTA_PROTEASOME_PATHWAY | WNT_SIGNALING | REACTOME_CROSS_PRESENTATION_OF_SOLUBLE_EXOGENOUS_ANTIGENS_ENDOSOMES | IIZUKA_LIVER_CANCER_PROGRESSION_L0_L1_DN | STONER_ESOPHAGEAL_CARCINOGENESIS_UP | TAVAZOIE_METASTASIS | DANG_MYC_TARGETS_DN | JOHANSSON_GLIOMAGENESIS_BY_PDGFB_UP | LIAO_HAVE_SOX4_BINDING_SITES | LEE_LIVER_CANCER_DENA_UP | KONDO_PROSTATE_CANCER_HCP_WITH_H3K27ME3 | SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_DN | LEE_LIVER_CANCER_ACOX1_UP | CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_DN | EBAUER_MYOGENIC_TARGETS_OF_PAX3_FOXO1_FUSION | ULE_SPLICING_VIA_NOVA2 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| MPEA | 0.55 | 0.6243 | 0.7273 | 0.6219 | 0.6973 | 0.5498 | 0.6250 | 0.576 | 0.5909 | 0.6154 | 0.5769 | 0.7674 | 0.5870 | 0.6218 | 0.5882 | 0.6471 | 0.7500 | 0.6418 | 0.6818 | 0.6250 | 0.5641 | 0.4444 | 0.6923 | 0.72 | 0.6245 | 0.6479 | 0.6667 | 0.6829 | 0.7308 | 0.5 | 0.6567 | 0.7273 | 0.7391 | 0.5451 | 0.6914 | 0.5971 | 0.6667 | 0.6393 | 0.5362 | 0.7097 | 0.6538 | 0.4545 | 0.7895 | 0.6 | 0.68 | 0.5811 | 0.5263 | 0.6064 | 0.5577 | 0.6538 | 0.60 | 0.52 | 0.6173 | 0.6285 | 0.7500 | 0.6429 | 0.6739 | 0.7083 | 0.6750 | 0.9444 | 0.6207 | 0.6216 | 0.7154 | 0.5759 | 0.7143 | 0.7179 | 0.6316 | 0.6410 | 0.6585 | 0.6346 | 0.6792 | 0.6944 | 0.6364 | 0.5730 | 0.7895 | 0.6609 | 0.5510 | 0.6099 | 0.6030 | 0.6250 | 0.5652 | 0.7922 | 0.6133 | 0.6667 | 0.7222 | 0.5484 | 0.6225 | 0.5928 | 0.5714 | 0.6627 | 0.6541 | 0.6538 | 0.7315 | 0.6013 | 0.7080 | 0.725 | 0.8125 | 0.6667 | 0.5625 | 0.650 | 0.500 | 0.5714 | 0.6396 | 0.5778 | 0.3684 | 0.6316 | 0.7048 | 0.5806 | 0.6333 | 0.625 | 0.6190 | 0.6170 | 0.6818 | 0.80 | 0.8889 | 0.6131 | 0.6096 | 0.7059 | 0.6818 | 0.8462 | 0.6935 | 0.7674 | 0.5882 | 0.6364 | 0.5970 | 0.6429 | 0.7500 | 0.55 | 0.6964 | 0.5128 | 0.6471 | 0.5778 | 0.5631 | 0.6154 | 0.5714 |
| GSEA | 0.40 | 0.4682 | 0.6364 | 0.4925 | 0.6122 | 0.4645 | 0.4674 | 0.448 | 0.4091 | 0.4615 | 0.4423 | 0.6279 | 0.4348 | 0.4958 | 0.3529 | 0.5294 | 0.4167 | 0.4955 | 0.5455 | 0.4375 | 0.5385 | 0.2963 | 0.6154 | 0.48 | 0.5217 | 0.5211 | 0.5897 | 0.5203 | 0.5769 | 0.5 | 0.4925 | 0.4545 | 0.5652 | 0.4549 | 0.6235 | 0.4532 | 0.4667 | 0.4918 | 0.4348 | 0.5806 | 0.5769 | 0.3636 | 0.6842 | 0.6 | 0.56 | 0.4717 | 0.4737 | 0.4787 | 0.4615 | 0.7308 | 0.55 | 0.38 | 0.5556 | 0.5217 | 0.5625 | 0.5357 | 0.5000 | 0.5417 | 0.5958 | 0.7222 | 0.5517 | 0.4595 | 0.6231 | 0.4643 | 0.5238 | 0.6410 | 0.5789 | 0.5385 | 0.5122 | 0.5385 | 0.5094 | 0.5000 | 0.5758 | 0.5056 | 0.7368 | 0.5460 | 0.4558 | 0.4709 | 0.5427 | 0.5312 | 0.5000 | 0.6753 | 0.4533 | 0.5714 | 0.7222 | 0.3978 | 0.4768 | 0.5090 | 0.3673 | 0.5754 | 0.5639 | 0.5385 | 0.6296 | 0.4695 | 0.5752 | 0.650 | 0.7500 | 0.5556 | 0.3750 | 0.575 | 0.425 | 0.4694 | 0.5635 | 0.4444 | 0.3158 | 0.4737 | 0.5619 | 0.5806 | 0.6667 | 0.500 | 0.6429 | 0.4681 | 0.5000 | 0.75 | 0.6111 | 0.4599 | 0.4813 | 0.7059 | 0.6364 | 0.7692 | 0.6452 | 0.6977 | 0.5294 | 0.5455 | 0.4179 | 0.5714 | 0.6944 | 0.45 | 0.6250 | 0.4872 | 0.4510 | 0.4667 | 0.4854 | 0.4872 | 0.4286 |
# t.test(enrichment_ratio_dcor,enrichment_ratio_ttest)
enrichment_ratios_percenages <- rbind(sum(enrichment_ratio_dcor>enrichment_ratio_ttest)/length(enrichment_ratio_dcor),
sum(enrichment_ratio_dcor<enrichment_ratio_ttest)/length(enrichment_ratio_dcor),
sum(enrichment_ratio_dcor==enrichment_ratio_ttest)/length(enrichment_ratio_dcor))*100
rownames(enrichment_ratios_percenages) <- c ( "More univariate enrichment detected in Dcor", "More univariate enrichment detected in T-test", "Draw" )
colnames(enrichment_ratios_percenages) <- "Percentage"
enrichment_ratios_percenages%>%
kable("html", digits = 4, longtable = TRUE) %>%
kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
row_spec(0, angle = -0)
| Percentage | |
|---|---|
| More univariate enrichment detected in Dcor | 94.0741 |
| More univariate enrichment detected in T-test | 2.2222 |
| Draw | 3.7037 |
enrichment_ratio_dcor <- NULL
enrichment_ratio_ttest <- NULL
for ( ii in 1:length(Significant_in_GSEA_not_in_dcor) ){
aux_genes <- intersect(pathway_collapsed[[Significant_in_GSEA_not_in_dcor[[ii]]]],colnames(expressions))
if ( identical(aux_genes, character(0))) next
aux_pathway_dcor <- dcor.test(dist(expressions[,aux_genes]),dist(genotypes),R=10000)
aux_individual_genes_in_pathway_dcor <- sapply(aux_genes,function(x) dcor.test(dist(expressions[,x]),dist(genotypes),R=10000)$p.value<0.05 )
aux_enrichment_ratio_dcor <- sum(aux_individual_genes_in_pathway_dcor)/length(aux_individual_genes_in_pathway_dcor)
enrichment_ratio_dcor[ii] <- aux_enrichment_ratio_dcor
aux_individual_genes_in_pathway_ttest <- sapply(aux_genes,function(x) t.test(expressions[,x]~genotypes)$p.value<0.05 )
aux_enrichment_ratio_ttest <- sum(aux_individual_genes_in_pathway_ttest)/length(aux_individual_genes_in_pathway_ttest)
aux_enrichment_ratio_ttest
enrichment_ratio_ttest[ii] <-aux_enrichment_ratio_ttest
}
enrichment_ratio_comparison <- rbind(enrichment_ratio_dcor,enrichment_ratio_ttest)
rownames(enrichment_ratio_comparison) <- c("MPEA","GSEA")
colnames(enrichment_ratio_comparison) <- Significant_in_GSEA_not_in_dcor
enrichment_ratio_comparison%>%
kable("html", digits = 4, longtable = TRUE) %>%
kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
row_spec(0, angle = -0)
| BOGNI_TREATMENT_RELATED_MYELOID_LEUKEMIA_DN | FAELT_B_CLL_WITH_VH_REARRANGEMENTS_DN | DACOSTA_UV_RESPONSE_VIA_ERCC3_COMMON_DN | PUJANA_BRCA2_PCC_NETWORK | KEGG_BASE_EXCISION_REPAIR | REACTOME_ANTIVIRAL_MECHANISM_BY_IFN_STIMULATED_GENES | REACTOME_CELL_CYCLE | GARY_CD5_TARGETS_DN | MARIADASON_RESPONSE_TO_BUTYRATE_SULINDAC_6 | DAZARD_RESPONSE_TO_UV_NHEK_DN | BENPORATH_PROLIFERATION | NUYTTEN_EZH2_TARGETS_DN | KEGG_B_CELL_RECEPTOR_SIGNALING_PATHWAY | REACTOME_REGULATION_OF_GLUCOKINASE_BY_GLUCOKINASE_REGULATORY_PROTEIN | RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_UP | RAMALHO_STEMNESS_UP | DING_LUNG_CANCER_EXPRESSION_BY_COPY_NUMBER | REACTOME_CELL_CYCLE_CHECKPOINTS | REACTOME_ANTIGEN_PROCESSING_UBIQUITINATION_PROTEASOME_DEGRADATION | GENTILE_UV_RESPONSE_CLUSTER_D8 | MORI_EMU_MYC_LYMPHOMA_BY_ONSET_TIME_UP | REACTOME_HIV_LIFE_CYCLE | FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_OK_VS_DONOR_UP | REACTOME_HIV_INFECTION | REACTOME_CHROMOSOME_MAINTENANCE | FIGUEROA_AML_METHYLATION_CLUSTER_1_DN | ZHANG_BREAST_CANCER_PROGENITORS_UP | PYEON_HPV_POSITIVE_TUMORS_UP | MOREAUX_MULTIPLE_MYELOMA_BY_TACI_DN | CHIANG_LIVER_CANCER_SUBCLASS_PROLIFERATION_UP | MARSON_BOUND_BY_E2F4_UNSTIMULATED | SHEN_SMARCA2_TARGETS_UP | GRADE_METASTASIS_DN | REACTOME_RESOLUTION_OF_AP_SITES_VIA_THE_MULTIPLE_NUCLEOTIDE_PATCH_REPLACEMENT_PATHWAY | REACTOME_BASE_EXCISION_REPAIR | REACTOME_CELL_CYCLE_MITOTIC | REACTOME_TRANSCRIPTION | KAUFFMANN_DNA_REPAIR_GENES | ZHAN_MULTIPLE_MYELOMA_CD1_VS_CD2_DN | KEGG_ANTIGEN_PROCESSING_AND_PRESENTATION | STARK_PREFRONTAL_CORTEX_22Q11_DELETION_UP | MITSIADES_RESPONSE_TO_APLIDIN_DN | REACTOME_HOST_INTERACTIONS_OF_HIV_FACTORS | BOYLAN_MULTIPLE_MYELOMA_C_D_UP | FEVR_CTNNB1_TARGETS_DN | REACTOME_NEP_NS2_INTERACTS_WITH_THE_CELLULAR_EXPORT_MACHINERY | REACTOME_TELOMERE_MAINTENANCE | BIDUS_METASTASIS_UP | ZHANG_TLX_TARGETS_36HR_DN | MARTINEZ_RESPONSE_TO_TRABECTEDIN_DN | SHAFFER_IRF4_TARGETS_IN_ACTIVATED_DENDRITIC_CELL | KIM_WT1_TARGETS_DN | MORI_PLASMA_CELL_DN | ENK_UV_RESPONSE_KERATINOCYTE_DN | ZHAN_EARLY_DIFFERENTIATION_GENES_DN | REACTOME_APC_C_CDC20_MEDIATED_DEGRADATION_OF_MITOTIC_PROTEINS | OISHI_CHOLANGIOMA_STEM_CELL_LIKE_UP | MATTIOLI_MGUS_VS_PCL | ABRAMSON_INTERACT_WITH_AIRE | ZHAN_MULTIPLE_MYELOMA_CD1_AND_CD2_UP | VILLANUEVA_LIVER_CANCER_KRT19_UP | REACTOME_LATE_PHASE_OF_HIV_LIFE_CYCLE | KEGG_SPLICEOSOME | MORI_MATURE_B_LYMPHOCYTE_DN | DITTMER_PTHLH_TARGETS_DN | CAIRO_HEPATOBLASTOMA_UP | BIOCARTA_BCR_PATHWAY | REACTOME_MRNA_PROCESSING | HAMAI_APOPTOSIS_VIA_TRAIL_UP | ROSS_AML_WITH_AML1_ETO_FUSION | REACTOME_GLUCOSE_TRANSPORT | REACTOME_APC_C_CDH1_MEDIATED_DEGRADATION_OF_CDC20_AND_OTHER_APC_C_CDH1_TARGETED_PROTEINS_IN_LATE_MITOSIS_EARLY_G1 | REACTOME_DEPOSITION_OF_NEW_CENPA_CONTAINING_NUCLEOSOMES_AT_THE_CENTROMERE | PECE_MAMMARY_STEM_CELL_DN | DAZARD_UV_RESPONSE_CLUSTER_G6 | GENTILE_UV_RESPONSE_CLUSTER_D4 | REACTOME_METABOLISM_OF_NON_CODING_RNA | REACTOME_REGULATION_OF_MITOTIC_CELL_CYCLE | KAMMINGA_EZH2_TARGETS | JOHNSTONE_PARVB_TARGETS_3_DN | HEDENFALK_BREAST_CANCER_BRCA1_VS_BRCA2 | BROWNE_HCMV_INFECTION_10HR_DN | PEART_HDAC_PROLIFERATION_CLUSTER_UP | PELLICCIOTTA_HDAC_IN_ANTIGEN_PRESENTATION_DN | REACTOME_P53_DEPENDENT_G1_DNA_DAMAGE_RESPONSE | GALE_APL_WITH_FLT3_MUTATED_UP | REACTOME_AUTODEGRADATION_OF_CDH1_BY_CDH1_APC_C | HAHTOLA_MYCOSIS_FUNGOIDES_CD4_DN | HEDENFALK_BREAST_CANCER_HEREDITARY_VS_SPORADIC | BIOCARTA_CARM_ER_PATHWAY | REACTOME_CLASS_I_MHC_MEDIATED_ANTIGEN_PROCESSING_PRESENTATION | VALK_AML_CLUSTER_10 | MILI_PSEUDOPODIA_HAPTOTAXIS_UP | HOLLEMAN_PREDNISOLONE_RESISTANCE_ALL_UP | BIOCARTA_PAR1_PATHWAY | SESTO_RESPONSE_TO_UV_C2 | CARD_MIR302A_TARGETS | REACTOME_SCF_BETA_TRCP_MEDIATED_DEGRADATION_OF_EMI1 | REACTOME_AUTODEGRADATION_OF_THE_E3_UBIQUITIN_LIGASE_COP1 | REACTOME_RNA_POL_I_RNA_POL_III_AND_MITOCHONDRIAL_TRANSCRIPTION | ELLWOOD_MYC_TARGETS_DN | BENPORATH_SOX2_TARGETS | KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_GAMMA_IN_WS | BROWNE_HCMV_INFECTION_4HR_DN | PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_UP | WAKASUGI_HAVE_ZNF143_BINDING_SITES | KIM_ALL_DISORDERS_CALB1_CORR_UP | ROESSLER_LIVER_CANCER_METASTASIS_DN | REACTOME_TRANSPORT_OF_MATURE_MRNA_DERIVED_FROM_AN_INTRONLESS_TRANSCRIPT | REACTOME_P53_INDEPENDENT_G1_S_DNA_DAMAGE_CHECKPOINT | REACTOME_NOTCH1_INTRACELLULAR_DOMAIN_REGULATES_TRANSCRIPTION | BENPORATH_ES_1 | PID_EPHA2_FWD_PATHWAY | REACTOME_RNA_POL_I_TRANSCRIPTION | YANG_BREAST_CANCER_ESR1_DN | REACTOME_MEIOSIS | REACTOME_REGULATION_OF_ORNITHINE_DECARBOXYLASE_ODC | BOYLAN_MULTIPLE_MYELOMA_C_UP | KEGG_SNARE_INTERACTIONS_IN_VESICULAR_TRANSPORT | HOLLMANN_APOPTOSIS_VIA_CD40_UP | WHITFIELD_CELL_CYCLE_G2_M | BRUINS_UVC_RESPONSE_MIDDLE | PID_P38_MK2_PATHWAY | KYNG_WERNER_SYNDROM_AND_NORMAL_AGING_UP | CHENG_IMPRINTED_BY_ESTRADIOL | GAZIN_EPIGENETIC_SILENCING_BY_KRAS | RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_MODERATELY_UP | TIEN_INTESTINE_PROBIOTICS_2HR_DN | ZUCCHI_METASTASIS_UP | PID_P53_REGULATION_PATHWAY | BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_CIS | REACTOME_TRANSPORT_OF_RIBONUCLEOPROTEINS_INTO_THE_HOST_NUCLEUS | KIM_GERMINAL_CENTER_T_HELPER_UP | PID_PS1_PATHWAY | OUILLETTE_CLL_13Q14_DELETION_UP | THUM_SYSTOLIC_HEART_FAILURE_DN | REACTOME_APOPTOSIS | PID_AR_NONGENOMIC_PATHWAY | ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_UP | JI_RESPONSE_TO_FSH_UP | BOYAULT_LIVER_CANCER_SUBCLASS_G1_UP | SIG_CHEMOTAXIS | BRUINS_UVC_RESPONSE_EARLY_LATE | LIN_MELANOMA_COPY_NUMBER_DN | REACTOME_ADAPTIVE_IMMUNE_SYSTEM | JOHNSTONE_PARVB_TARGETS_2_DN | ACEVEDO_LIVER_CANCER_UP | KYNG_ENVIRONMENTAL_STRESS_RESPONSE_UP | LAIHO_COLORECTAL_CANCER_SERRATED_DN | PID_HEDGEHOG_GLI_PATHWAY | LINDGREN_BLADDER_CANCER_WITH_LOH_IN_CHR9Q | LIN_MELANOMA_COPY_NUMBER_UP | DAVICIONI_MOLECULAR_ARMS_VS_ERMS_UP | HAHTOLA_MYCOSIS_FUNGOIDES_SKIN_UP | BIOCARTA_TFF_PATHWAY | HOSHIDA_LIVER_CANCER_SUBCLASS_S2 | BENPORATH_OCT4_TARGETS | GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_UP | GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN | SETLUR_PROSTATE_CANCER_TMPRSS2_ERG_FUSION_UP | GEORGES_TARGETS_OF_MIR192_AND_MIR215 | KUROKAWA_LIVER_CANCER_CHEMOTHERAPY_DN | BILD_E2F3_ONCOGENIC_SIGNATURE | LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN | WOOD_EBV_EBNA1_TARGETS_DN | BENPORATH_NANOG_TARGETS | WINTER_HYPOXIA_DN | IKEDA_MIR30_TARGETS_UP | REACTOME_NRAGE_SIGNALS_DEATH_THROUGH_JNK | KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_UV_IN_OLD | HASLINGER_B_CLL_WITH_6Q21_DELETION | BIOCARTA_WNT_PATHWAY | YAGI_AML_WITH_T_9_11_TRANSLOCATION | HIRSCH_CELLULAR_TRANSFORMATION_SIGNATURE_DN | BIOCARTA_CXCR4_PATHWAY | TAYLOR_METHYLATED_IN_ACUTE_LYMPHOBLASTIC_LEUKEMIA | GINESTIER_BREAST_CANCER_20Q13_AMPLIFICATION_UP | ZHANG_RESPONSE_TO_IKK_INHIBITOR_AND_TNF_DN | ZHAN_MULTIPLE_MYELOMA_HP_UP | REACTOME_SMAD2_SMAD3_SMAD4_HETEROTRIMER_REGULATES_TRANSCRIPTION | MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_DN | VANHARANTA_UTERINE_FIBROID_WITH_7Q_DELETION_UP | ONKEN_UVEAL_MELANOMA_UP | BILBAN_B_CLL_LPL_UP | CHEN_NEUROBLASTOMA_COPY_NUMBER_GAINS | KEGG_NOTCH_SIGNALING_PATHWAY | HADDAD_T_LYMPHOCYTE_AND_NK_PROGENITOR_UP | LEE_CALORIE_RESTRICTION_MUSCLE_DN | KYNG_DNA_DAMAGE_BY_GAMMA_AND_UV_RADIATION | KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS | KATSANOU_ELAVL1_TARGETS_DN | GYORFFY_MITOXANTRONE_RESISTANCE | MULLIGHAN_NPM1_SIGNATURE_3_DN | JIANG_TIP30_TARGETS_UP | REACTOME_APOPTOTIC_CLEAVAGE_OF_CELLULAR_PROTEINS | GRYDER_PAX3FOXO1_ENHANCERS_KO_DOWN | CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_2 | HOFMANN_CELL_LYMPHOMA_UP | STAMBOLSKY_RESPONSE_TO_VITAMIN_D3_UP | ABBUD_LIF_SIGNALING_1_UP | DEBOSSCHER_NFKB_TARGETS_REPRESSED_BY_GLUCOCORTICOIDS | CHEOK_RESPONSE_TO_HD_MTX_UP | REACTOME_PHASE1_FUNCTIONALIZATION_OF_COMPOUNDS | VERHAAK_AML_WITH_NPM1_MUTATED_UP | PID_INTEGRIN_CS_PATHWAY | PID_UPA_UPAR_PATHWAY | REACTOME_COLLAGEN_FORMATION | DALESSIO_TSA_RESPONSE | GUENTHER_GROWTH_SPHERICAL_VS_ADHERENT_DN | VERRECCHIA_EARLY_RESPONSE_TO_TGFB1 | BIOCARTA_DC_PATHWAY | NAKAJIMA_MAST_CELL | REACTOME_CYTOCHROME_P450_ARRANGED_BY_SUBSTRATE_TYPE | KIM_ALL_DISORDERS_CALB1_CORR_DN | GOLUB_ALL_VS_AML_DN | PID_INTEGRIN2_PATHWAY | HESS_TARGETS_OF_HOXA9_AND_MEIS1_DN | LIAN_NEUTROPHIL_GRANULE_CONSTITUENTS | KRIEG_HYPOXIA_VIA_KDM3A | PID_SYNDECAN_1_PATHWAY | PARK_APL_PATHOGENESIS_DN | HWANG_PROSTATE_CANCER_MARKERS | ALONSO_METASTASIS_NEURAL_UP | AMIT_EGF_RESPONSE_120_MCF10A | LI_CISPLATIN_RESISTANCE_DN | REACTOME_CELL_SURFACE_INTERACTIONS_AT_THE_VASCULAR_WALL | VERRECCHIA_RESPONSE_TO_TGFB1_C2 | GROSS_ELK3_TARGETS_DN | ALTEMEIER_RESPONSE_TO_LPS_WITH_MECHANICAL_VENTILATION | NABA_COLLAGENS | GHANDHI_BYSTANDER_IRRADIATION_UP | KOHOUTEK_CCNT1_TARGETS | TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_HSC_DN | KOBAYASHI_EGFR_SIGNALING_6HR_DN | REACTOME_TRANSPORT_OF_GLUCOSE_AND_OTHER_SUGARS_BILE_SALTS_AND_ORGANIC_ACIDS_METAL_IONS_AND_AMINE_COMPOUNDS | SARTIPY_NORMAL_AT_INSULIN_RESISTANCE_UP | REACTOME_EXTRACELLULAR_MATRIX_ORGANIZATION | MIKKELSEN_MCV6_ICP_WITH_H3K27ME3 | VART_KSHV_INFECTION_ANGIOGENIC_MARKERS_UP | KEGG_ARACHIDONIC_ACID_METABOLISM | KANG_AR_TARGETS_UP | ZHAN_MULTIPLE_MYELOMA_CD1_VS_CD2_UP | CHEN_LVAD_SUPPORT_OF_FAILING_HEART_UP | HOLLERN_MICROACINAR_BREAST_TUMOR_UP | WANG_BARRETTS_ESOPHAGUS_AND_ESOPHAGUS_CANCER_DN | MIKKELSEN_MEF_ICP_WITH_H3K27ME3 | GHANDHI_DIRECT_IRRADIATION_UP | BIOCARTA_CYTOKINE_PATHWAY | MIKKELSEN_MEF_LCP_WITH_H3K27ME3 | YAO_HOXA10_TARGETS_VIA_PROGESTERONE_UP | VERRECCHIA_RESPONSE_TO_TGFB1_C1 | PID_RXR_VDR_PATHWAY | XU_HGF_SIGNALING_NOT_VIA_AKT1_6HR | WANG_CLASSIC_ADIPOGENIC_TARGETS_OF_PPARG | KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_LACTO_AND_NEOLACTO_SERIES | HUPER_BREAST_BASAL_VS_LUMINAL_UP | NAKAYAMA_SOFT_TISSUE_TUMORS_PCA2_DN | JEON_SMAD6_TARGETS_UP | PEPPER_CHRONIC_LYMPHOCYTIC_LEUKEMIA_UP | PID_INTEGRIN5_PATHWAY | BIOCARTA_STEM_PATHWAY | NAKAMURA_ADIPOGENESIS_EARLY_UP | BIOCARTA_INFLAM_PATHWAY | BERENJENO_ROCK_SIGNALING_NOT_VIA_RHOA_UP | REACTOME_INTEGRIN_CELL_SURFACE_INTERACTIONS | KHETCHOUMIAN_TRIM24_TARGETS_UP | NAKAJIMA_EOSINOPHIL | SEMENZA_HIF1_TARGETS | MOREAUX_B_LYMPHOCYTE_MATURATION_BY_TACI_UP | AMIT_EGF_RESPONSE_120_HELA | YANG_MUC2_TARGETS_DUODENUM_6MO_DN | FIGUEROA_AML_METHYLATION_CLUSTER_5_DN | REACTOME_AMINE_LIGAND_BINDING_RECEPTORS | SABATES_COLORECTAL_ADENOMA_UP | PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_DN | SUZUKI_RESPONSE_TO_TSA_AND_DECITABINE_1A | MADAN_DPPA4_TARGETS | URS_ADIPOCYTE_DIFFERENTIATION_UP | ONDER_CDH1_SIGNALING_VIA_CTNNB1 | KERLEY_RESPONSE_TO_CISPLATIN_UP | CREIGHTON_AKT1_SIGNALING_VIA_MTOR_UP | MEISSNER_NPC_HCP_WITH_H3K4ME2_AND_H3K27ME3 | LABBE_TARGETS_OF_TGFB1_AND_WNT3A_DN | SAKAI_CHRONIC_HEPATITIS_VS_LIVER_CANCER_DN | MARKEY_RB1_CHRONIC_LOF_DN | SHEN_SMARCA2_TARGETS_DN | NABA_ECM_AFFILIATED | KIM_LIVER_CANCER_POOR_SURVIVAL_DN | REACTOME_CLASS_B_2_SECRETIN_FAMILY_RECEPTORS | MARTENS_TRETINOIN_RESPONSE_UP | WATANABE_COLON_CANCER_MSI_VS_MSS_UP | MOREAUX_MULTIPLE_MYELOMA_BY_TACI_UP | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| MPEA | 0.5714 | 0.6316 | 0.7464 | 0.7375 | 0.7308 | 0.7021 | 0.7366 | 0.6789 | 0.7826 | 0.8114 | 0.7674 | NA | 0.6406 | 0.7368 | 0.7193 | 0.7227 | 0.8000 | 0.7386 | 0.7368 | 0.6970 | 0.6981 | 0.6947 | NA | 0.6890 | 0.8154 | 0.5238 | 0.7402 | 0.7297 | 0.8133 | 0.7701 | NA | 0.7982 | 0.6897 | NA | 0.7500 | 0.7254 | 0.7557 | 0.6815 | 0.5417 | 0.7049 | 0.6238 | 0.7407 | 0.68 | 0.6154 | NA | 0.7368 | 0.8636 | 0.7570 | 0.6932 | 0.6864 | 0.6591 | 0.6914 | 0.8333 | 0.7201 | 0.6667 | 0.8182 | 0.6743 | 0.6623 | 0.7667 | 0.6154 | 0.6883 | 0.6988 | 0.8182 | 0.7321 | 0.6949 | 0.6296 | 0.5938 | 0.77 | NA | 0.5581 | 0.7407 | 0.7963 | 0.8846 | 0.6620 | 0.8585 | 0.8605 | 0.7407 | 0.7812 | 0.8214 | NA | 0.6535 | 0.7111 | 0.5957 | 0.7297 | 0.6531 | 0.7742 | 0.7917 | 0.716 | 0.6154 | 0.7083 | 0.7266 | 0.7407 | NA | NA | 0.5882 | 0.6512 | 0.6415 | 0.7500 | 0.7209 | 0.7727 | 0.60 | NA | 0.750 | 0.6863 | 0.5833 | 0.6977 | NA | 0.8333 | 0.7273 | 0.7556 | 0.8696 | 0.6806 | 0.3125 | 0.8000 | 0.5263 | 0.7869 | 0.7778 | 0.8095 | 0.6364 | 0.6493 | 0.7190 | 0.6154 | 0.6 | 0.7167 | 0.5532 | NA | 0.7059 | 0.6545 | 0.7241 | 0.6744 | 0.6786 | 0.7368 | 0.6154 | 0.6129 | 0.6087 | 0.61 | 0.664 | 0.5667 | 0.6824 | 0.6615 | 0.6133 | 0.700 | 0.6331 | 0.6786 | NA | 0.6829 | NA | 0.6889 | 0.6000 | 0.6571 | 0.6825 | 0.5676 | 0.6225 | 0.7714 | 0.45 | 0.6832 | 0.6536 | 0.7273 | NA | 0.6909 | NA | 0.5556 | 0.6261 | NA | 0.6 | NA | 0.5806 | 0.6098 | 0.4815 | 0.6250 | 0.7059 | 0.6522 | 0.6204 | 0.6232 | 0.5909 | 0.5455 | 0.6415 | 0.5306 | 0.6923 | 0.6818 | 0.7326 | 0.6486 | NA | 0.6522 | 0.7059 | 0.6296 | 0.6833 | 0.5814 | 0.5634 | 0.6706 | 0.5432 | 0.7692 | 0.6881 | 0.7027 | 0.7273 | 0.5887 | 0.6364 | 0.6522 | 0.6863 | 0.7500 | 0.6190 | 0.8421 | 0.6038 | 0.7820 | 0.72 | 0.6389 | 0.5814 | 0.4706 | 0.6957 | 0.6327 | 0.6667 | 0.7368 | 0.6316 | 0.6364 | 1 | 0.8750 | 0.5667 | 0.5789 | 0.6111 | 0.5714 | 0.6905 | 0.5652 | NA | 0.68 | 0.65 | 0.6250 | 0.6190 | 0.6667 | 0.6556 | 0.6 | 0.6964 | 0.6071 | 0.6222 | 0.5000 | 0.6047 | 0.75 | 0.6119 | 0.6000 | 0.6183 | 0.8108 | NA | 0.6061 | 0.6184 | 0.6111 | 0.7742 | 0.6125 | 0.5909 | 0.7368 | 0.6087 | 0.6667 | 0.6875 | 0.6667 | 0.7 | 0.625 | 0.6471 | 0.6098 | 0.6000 | 0.4737 | 0.8182 | 0.7059 | NA | 0.6444 | 0.5926 | 0.5000 | 0.6667 | 0.5610 | 0.7083 | 0.5806 | 0.7091 | 0.6875 | NA | 0.5652 | 0.7143 | 0.6104 | 0.5685 | 0.65 | 0.5294 | 0.7018 | 0.6316 | 0.6364 | 0.7917 | 0.6258 | 0.5802 | 0.6897 | 0.6575 | 0.6442 | 0.5270 | 0.5882 | 0.6102 | NA | 0.6111 | 0.6492 |
| GSEA | 0.5357 | 0.6316 | 0.6599 | 0.6844 | 0.6923 | 0.6809 | 0.6831 | 0.5826 | 0.6957 | 0.7105 | 0.7558 | NA | 0.6094 | 0.7368 | 0.6316 | 0.5798 | 0.6364 | 0.6932 | 0.5877 | 0.6061 | 0.5849 | 0.6105 | NA | 0.6037 | 0.7538 | 0.4762 | 0.6716 | 0.6757 | 0.7067 | 0.7356 | NA | 0.6906 | 0.6207 | NA | 0.6875 | 0.6580 | 0.6641 | 0.5924 | 0.3750 | 0.6066 | 0.6139 | 0.6728 | 0.62 | 0.5385 | NA | 0.7368 | 0.8182 | 0.7196 | 0.6250 | 0.6213 | 0.5909 | 0.5688 | 0.7778 | 0.6412 | 0.5897 | 0.7273 | 0.5486 | 0.5974 | 0.7333 | 0.5385 | 0.6364 | 0.6145 | 0.7576 | 0.6607 | 0.6271 | 0.5481 | 0.5312 | 0.72 | NA | 0.4884 | 0.7037 | 0.7037 | 0.8462 | 0.5211 | 0.7358 | 0.7907 | 0.7407 | 0.7031 | 0.7143 | NA | 0.6142 | 0.6222 | 0.5957 | 0.6757 | 0.6122 | 0.7097 | 0.7083 | 0.679 | 0.5385 | 0.6667 | 0.5899 | 0.7037 | NA | NA | 0.5000 | 0.4884 | 0.5660 | 0.6818 | 0.6512 | 0.6818 | 0.55 | NA | 0.625 | 0.5686 | 0.5139 | 0.6512 | NA | 0.7083 | 0.7727 | 0.6889 | 0.7391 | 0.5787 | 0.2500 | 0.7333 | 0.3684 | 0.6721 | 0.6889 | 0.6667 | 0.4545 | 0.5821 | 0.6281 | 0.5128 | 0.5 | 0.6667 | 0.4255 | NA | 0.5882 | 0.6000 | 0.4138 | 0.6047 | 0.5357 | 0.6842 | 0.5385 | 0.6452 | 0.4348 | 0.52 | 0.560 | 0.4333 | 0.4941 | 0.5231 | 0.5600 | 0.625 | 0.5468 | 0.5357 | NA | 0.5793 | NA | 0.6444 | 0.5333 | 0.5143 | 0.5556 | 0.4865 | 0.5000 | 0.7238 | 0.45 | 0.6040 | 0.5556 | 0.7273 | NA | 0.5818 | NA | 0.4074 | 0.5130 | NA | 0.6 | NA | 0.5161 | 0.5122 | 0.4074 | 0.5625 | 0.6471 | 0.6957 | 0.5648 | 0.5362 | 0.5455 | 0.5152 | 0.5094 | 0.4490 | 0.6538 | 0.6364 | 0.6395 | 0.4595 | NA | 0.5217 | 0.5588 | 0.4444 | 0.6167 | 0.4651 | 0.4366 | 0.5176 | 0.5185 | 0.5000 | 0.5780 | 0.5405 | 0.6364 | 0.4762 | 0.5000 | 0.6087 | 0.5490 | 0.6875 | 0.5238 | 0.7368 | 0.5094 | 0.6992 | 0.68 | 0.4722 | 0.4186 | 0.4706 | 0.6087 | 0.4694 | 0.6111 | 0.6579 | 0.5263 | 0.5758 | 1 | 0.6667 | 0.5500 | 0.5789 | 0.4722 | 0.4524 | 0.6429 | 0.4348 | NA | 0.64 | 0.50 | 0.5972 | 0.4286 | 0.6667 | 0.5333 | 0.4 | 0.5179 | 0.5714 | 0.5333 | 0.4375 | 0.5349 | 0.60 | 0.4478 | 0.4333 | 0.4962 | 0.6486 | NA | 0.4242 | 0.5263 | 0.5556 | 0.6452 | 0.4500 | 0.4848 | 0.4737 | 0.3913 | 0.5000 | 0.5625 | 0.4583 | 0.6 | 0.375 | 0.5294 | 0.5854 | 0.4182 | 0.4211 | 0.5909 | 0.5294 | NA | 0.5778 | 0.4444 | 0.4444 | 0.5556 | 0.5122 | 0.6667 | 0.5484 | 0.5455 | 0.6042 | NA | 0.4348 | 0.5714 | 0.5065 | 0.4932 | 0.55 | 0.4118 | 0.4912 | 0.5614 | 0.5152 | 0.7500 | 0.5355 | 0.4444 | 0.5172 | 0.5205 | 0.4615 | 0.3649 | 0.4118 | 0.5085 | NA | 0.5556 | 0.4839 |
t.test(enrichment_ratio_dcor,enrichment_ratio_ttest)
##
## Welch Two Sample t-test
##
## data: enrichment_ratio_dcor and enrichment_ratio_ttest
## t = 11.354, df = 518.55, p-value < 2.2e-16
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
## 0.07723829 0.10955945
## sample estimates:
## mean of x mean of y
## 0.6730257 0.5796268
enrichment_ratios_percenages <- rbind(sum(enrichment_ratio_dcor>enrichment_ratio_ttest,na.rm = T)/length(enrichment_ratio_dcor),
sum(enrichment_ratio_dcor<enrichment_ratio_ttest,na.rm = T)/length(enrichment_ratio_dcor),
sum(enrichment_ratio_dcor==enrichment_ratio_ttest,na.rm = T)/length(enrichment_ratio_dcor))*100
rownames(enrichment_ratios_percenages) <- c ( "More univariate enrichment detected in Dcor", "More univariate enrichment detected in T-test", "Draw" )
colnames(enrichment_ratios_percenages) <- "Percentage"
enrichment_ratios_percenages%>%
kable("html", digits = 4, longtable = TRUE) %>%
kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
row_spec(0, angle = -0)
| Percentage | |
|---|---|
| More univariate enrichment detected in Dcor | 86.6438 |
| More univariate enrichment detected in T-test | 1.0274 |
| Draw | 4.1096 |
# stopCluster(cl)
library(ggfortify)
## Loading required package: ggplot2
for (name in (sort(Significant_in_dcor_not_in_GSEA, decreasing = F))){
strongestpathwaydcor <- unname(unlist(pathway_collapsed[name]))
expressions_pathway <- as.data.frame(expressions[,which(colnames(expressions)%in% strongestpathwaydcor)])
genotypes_category <- ifelse(genotypes==1, "MUT", "WT")
genotypes_category <- as.data.frame(genotypes_category)
print(name)
print(autoplot(prcomp(expressions_pathway), data = genotypes_category, colour='genotypes_category' )+theme_bw()+ggtitle(label = "name"))
# pcoa.obj <- pcoa(D = dist(expressions_pathway), correction="none", rn=NULL)
# biplot.pcoa(pcoa.obj)
}
## [1] "AIGNER_ZEB1_TARGETS"
## [1] "ALFANO_MYC_TARGETS"
## [1] "AMIT_SERUM_RESPONSE_240_MCF10A"
## [1] "AMIT_SERUM_RESPONSE_480_MCF10A"
## [1] "BANDRES_RESPONSE_TO_CARMUSTIN_WITHOUT_MGMT_48HR_UP"
## [1] "BAUS_TFF2_TARGETS_UP"
## [1] "BECKER_TAMOXIFEN_RESISTANCE_DN"
## [1] "BIOCARTA_PROTEASOME_PATHWAY"
## [1] "BOCHKIS_FOXA2_TARGETS"
## [1] "BONOME_OVARIAN_CANCER_SURVIVAL_OPTIMAL_DEBULKING"
## [1] "BOYAULT_LIVER_CANCER_SUBCLASS_G5_DN"
## [1] "BOYAULT_LIVER_CANCER_SUBCLASS_G6_UP"
## [1] "BROWNE_HCMV_INFECTION_48HR_UP"
## [1] "BURTON_ADIPOGENESIS_11"
## [1] "BURTON_ADIPOGENESIS_7"
## [1] "CHANG_IMMORTALIZED_BY_HPV31_UP"
## [1] "CHENG_RESPONSE_TO_NICKEL_ACETATE"
## [1] "CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_DN"
## [1] "CHIANG_LIVER_CANCER_SUBCLASS_INTERFERON_DN"
## [1] "CHIARETTI_T_ALL_REFRACTORY_TO_THERAPY"
## [1] "COATES_MACROPHAGE_M1_VS_M2_DN"
## [1] "DACOSTA_UV_RESPONSE_VIA_ERCC3_TTD_UP"
## [1] "DANG_MYC_TARGETS_DN"
## [1] "DAWSON_METHYLATED_IN_LYMPHOMA_TCL1"
## [1] "DE_YY1_TARGETS_DN"
## [1] "DELACROIX_RAR_BOUND_ES"
## [1] "DELLA_RESPONSE_TO_TSA_AND_BUTYRATE"
## [1] "DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_UP"
## [1] "DUTERTRE_ESTRADIOL_RESPONSE_6HR_DN"
## [1] "EBAUER_MYOGENIC_TARGETS_OF_PAX3_FOXO1_FUSION"
## [1] "EBAUER_TARGETS_OF_PAX3_FOXO1_FUSION_UP"
## [1] "FERRANDO_HOX11_NEIGHBORS"
## [1] "FUJII_YBX1_TARGETS_DN"
## [1] "GAVIN_FOXP3_TARGETS_CLUSTER_P2"
## [1] "GRADE_COLON_VS_RECTAL_CANCER_DN"
## [1] "GRAHAM_CML_QUIESCENT_VS_NORMAL_QUIESCENT_DN"
## [1] "GRESHOCK_CANCER_COPY_NUMBER_UP"
## [1] "HANN_RESISTANCE_TO_BCL2_INHIBITOR_UP"
## [1] "HECKER_IFNB1_TARGETS"
## [1] "HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_UP"
## [1] "HOELZEL_NF1_TARGETS_DN"
## [1] "HOLLERN_EMT_BREAST_TUMOR_DN"
## [1] "HOSHIDA_LIVER_CANCER_LATE_RECURRENCE_UP"
## [1] "IIZUKA_LIVER_CANCER_PROGRESSION_L0_L1_DN"
## [1] "INGRAM_SHH_TARGETS_DN"
## [1] "ISSAEVA_MLL2_TARGETS"
## [1] "IVANOVA_HEMATOPOIESIS_STEM_CELL_SHORT_TERM"
## [1] "JAEGER_METASTASIS_UP"
## [1] "JI_METASTASIS_REPRESSED_BY_STK11"
## [1] "JOHANSSON_GLIOMAGENESIS_BY_PDGFB_UP"
## [1] "JOHNSTONE_PARVB_TARGETS_3_UP"
## [1] "KAMMINGA_SENESCENCE"
## [1] "KEGG_PROTEASOME"
## [1] "KONDO_PROSTATE_CANCER_HCP_WITH_H3K27ME3"
## [1] "KUMAR_TARGETS_OF_MLL_AF9_FUSION"
## [1] "LABBE_WNT3A_TARGETS_DN"
## [1] "LEE_LIVER_CANCER_ACOX1_UP"
## [1] "LEE_LIVER_CANCER_DENA_UP"
## [1] "LIAO_HAVE_SOX4_BINDING_SITES"
## [1] "LIU_SOX4_TARGETS_UP"
## [1] "LIU_VAV3_PROSTATE_CARCINOGENESIS_UP"
## [1] "LU_TUMOR_ANGIOGENESIS_UP"
## [1] "MAHADEVAN_IMATINIB_RESISTANCE_DN"
## [1] "MANN_RESPONSE_TO_AMIFOSTINE_UP"
## [1] "MARIADASON_REGULATED_BY_HISTONE_ACETYLATION_DN"
## [1] "MARSON_FOXP3_TARGETS_STIMULATED_UP"
## [1] "MIKKELSEN_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3"
## [1] "MISHRA_CARCINOMA_ASSOCIATED_FIBROBLAST_DN"
## [1] "MORI_LARGE_PRE_BII_LYMPHOCYTE_DN"
## [1] "NIELSEN_GIST_AND_SYNOVIAL_SARCOMA_DN"
## [1] "NUTT_GBM_VS_AO_GLIOMA_UP"
## [1] "ONDER_CDH1_TARGETS_2_UP"
## [1] "ONO_AML1_TARGETS_DN"
## [1] "ONO_FOXP3_TARGETS_DN"
## [1] "PASINI_SUZ12_TARGETS_UP"
## [1] "PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_4"
## [1] "PENG_RAPAMYCIN_RESPONSE_UP"
## [1] "PETRETTO_CARDIAC_HYPERTROPHY"
## [1] "PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_UP"
## [1] "PLASARI_TGFB1_TARGETS_10HR_DN"
## [1] "POOLA_INVASIVE_BREAST_CANCER_UP"
## [1] "QI_PLASMACYTOMA_UP"
## [1] "REACTOME_CHEMOKINE_RECEPTORS_BIND_CHEMOKINES"
## [1] "REACTOME_CLASS_A1_RHODOPSIN_LIKE_RECEPTORS"
## [1] "REACTOME_CROSS_PRESENTATION_OF_SOLUBLE_EXOGENOUS_ANTIGENS_ENDOSOMES"
## [1] "REACTOME_DEVELOPMENTAL_BIOLOGY"
## [1] "REACTOME_G_ALPHA_I_SIGNALLING_EVENTS"
## [1] "REACTOME_L1CAM_INTERACTIONS"
## [1] "REACTOME_MYOGENESIS"
## [1] "REACTOME_NEPHRIN_INTERACTIONS"
## [1] "REACTOME_PEPTIDE_LIGAND_BINDING_RECEPTORS"
## [1] "REACTOME_REGULATION_OF_SIGNALING_BY_CBL"
## [1] "REACTOME_SYNTHESIS_OF_PIPS_AT_THE_PLASMA_MEMBRANE"
## [1] "RIGGI_EWING_SARCOMA_PROGENITOR_DN"
## [1] "RIZKI_TUMOR_INVASIVENESS_3D_UP"
## [1] "ROME_INSULIN_TARGETS_IN_MUSCLE_DN"
## [1] "RORIE_TARGETS_OF_EWSR1_FLI1_FUSION_DN"
## [1] "ROY_WOUND_BLOOD_VESSEL_DN"
## [1] "SANSOM_APC_TARGETS_DN"
## [1] "SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP"
## [1] "SCHLOSSER_MYC_AND_SERUM_RESPONSE_SYNERGY"
## [1] "SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_DN"
## [1] "SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP"
## [1] "SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN"
## [1] "SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A12"
## [1] "SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A5"
## [1] "SIMBULAN_PARP1_TARGETS_DN"
## [1] "SIMBULAN_UV_RESPONSE_IMMORTALIZED_DN"
## [1] "SMID_BREAST_CANCER_NORMAL_LIKE_UP"
## [1] "SMID_BREAST_CANCER_RELAPSE_IN_BONE_DN"
## [1] "STONER_ESOPHAGEAL_CARCINOGENESIS_UP"
## [1] "TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_DN"
## [1] "TAVAZOIE_METASTASIS"
## [1] "TSENG_ADIPOGENIC_POTENTIAL_UP"
## [1] "ULE_SPLICING_VIA_NOVA2"
## [1] "VALK_AML_CLUSTER_15"
## [1] "VANTVEER_BREAST_CANCER_BRCA1_UP"
## [1] "VECCHI_GASTRIC_CANCER_EARLY_DN"
## [1] "VERHAAK_AML_WITH_NPM1_MUTATED_DN"
## [1] "VERHAAK_GLIOBLASTOMA_PRONEURAL"
## [1] "WIELAND_UP_BY_HBV_INFECTION"
## [1] "WNT_SIGNALING"
## [1] "WONG_IFNA2_RESISTANCE_DN"
## [1] "WOO_LIVER_CANCER_RECURRENCE_UP"
## [1] "XU_CREBBP_TARGETS_DN"
## [1] "XU_GH1_AUTOCRINE_TARGETS_UP"
## [1] "YAGI_AML_WITH_11Q23_REARRANGED"
## [1] "YAMAZAKI_TCEB3_TARGETS_DN"
## [1] "YANG_BREAST_CANCER_ESR1_LASER_DN"
## [1] "YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_9"
## [1] "ZHAN_MULTIPLE_MYELOMA_CD2_UP"
## [1] "ZHAN_MULTIPLE_MYELOMA_HP_DN"
## [1] "ZHAN_V1_LATE_DIFFERENTIATION_GENES_UP"
## [1] "ZHENG_FOXP3_TARGETS_IN_THYMUS_UP"
## [1] "ZHU_CMV_24_HR_DN"
# rownames(gsea_results_significant)
# for (name in (Significant_in_GSEA_not_in_dcor)){
# strongestpathwaydcor <- unname(unlist(pathway_collapsed[name]))
# expressions_pathway <- as.data.frame(expressions[,which(colnames(expressions)%in% strongestpathwaydcor)])
# genotypes_category <- ifelse(genotypes==1, "MUT", "WT")
# genotypes_category <- as.data.frame(genotypes_category)
# print(name)
# print(autoplot(prcomp(expressions_pathway), data = genotypes_category, colour='genotypes_category' )+theme_bw()+ggtitle(label = "name"))
#
# # pcoa.obj <- pcoa(D = dist(expressions_pathway), correction="none", rn=NULL)
# # biplot.pcoa(pcoa.obj)
# }